Changes between Version 82 and Version 83 of Release1.4


Ignore:
Timestamp:
Apr 15, 2009, 10:52:09 AM (17 years ago)
Author:
Scooter Morris
Comment:

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  • Release1.4

    v82 v83  
    1111 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 #7165
    1212  * Use will specify bond length, angle and dihedral
    13  1. Minimize Structure: don't call Dock Prep again if all atoms already have amberType and topology has not changed. ECM
    14  1. ~~(planned/probable) Measure planes. EFP~~ unlikely due to several features (some new) still needed for Axes
    15  1. (planned/probable) Rename models using Model Panel. EFP
    16  1. (planned/probable) Coulombic surface coloring. EFP
    17  1. move Molecule color to Model GC
    18  1. Need "effects" command for controlling all Effects via script. ECM
    19  1. Reduce mmcif template file download
    20  1. Framework for invoking chimeraservices.rbvi.ucsf.edu and other web services CH
     13 1. Minimize Structure: don't call Dock Prep again if all atoms already have amberType and topology has not changed. Ticket #7166
     14 1. ~~(planned/probable) Measure planes. EFP~~ unlikely due to several features (some new) still needed for Axes. Ticket #7167
     15 1. (planned/probable) Rename models using Model Panel. Ticket #7168
     16 1. (planned/probable) Coulombic surface coloring. Ticket #7051
     17 1. move Molecule color to Model Ticket #7052
     18 1. Need "effects" command for controlling all Effects via script. Ticket #7053
     19 1. Reduce mmcif template file download Ticket #7054
     20 1. Framework for invoking chimeraservices.rbvi.ucsf.edu and other web services Ticket #7055
    2121  *  Security, transactions with IDs
    22  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. ECM
    23   * (search other databases such as NR? PSI-BLAST on NR?)
    24  1. Support PDB v3.2
     22 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
     23  * (search other databases such as NR? PSI-BLAST on NR?) Ticket #7170
     24 1. Support PDB v3.2 Ticket #7056
    2525
    2626== Features Desired for 1.4 ==
    2727These 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.
    28  1. Distribute smaller mmcif template file, but provide a location for users to download the full template file from our web site
     28 1. Distribute smaller mmcif template file, but provide a location for users to download the full template file from our web site Ticket #7171
    2929  * Implement cron job to continuously update mmcif template file
    30  1. Output compressed TIFF instead of current giant files. ECM
    31  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.
    32  1. Reposition normal labels with mouse. EFP
    33  1. (planned/probable) Finish Color Key (X3D output [needed for raytracing]; "key" option to rangecolor command). EFP
    34  1. Interpolating ribbons GC
    35  1. Integration/addition of a 2D plotting library (e.g. matplotlib)
    36  1. Change depth cueing ramp parameter
    37  1. Better label-offset algorithm, particularly when zooming
     30 1. Output compressed TIFF instead of current giant files. Ticket #7172
     31 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
     32 1. Reposition normal labels with mouse. Ticket #7174
     33 1. (planned/probable) Finish Color Key (X3D output [needed for raytracing]; "key" option to rangecolor command). Ticket #7175
     34 1. Interpolating ribbons Ticket #7176
     35 1. Integration/addition of a 2D plotting library (e.g. matplotlib) Ticket #7177
     36 1. Change depth cueing ramp parameter Ticket #7178
     37 1. Better label-offset algorithm, particularly when zooming Ticket #7179
    3838
    3939
    4040=== Documentation ===
    4141
    42  1. Need new image-making tutorial(s) in addition to or replacing the current one. ECM
     42 1. Need new image-making tutorial(s) in addition to or replacing the current one. Ticket #7180
    4343
    44 === Core 2 ===
    45  1. Electron tomography: Visualization of objects embedded in membranes e.g. nuclear pores in nuclear envelope, spikes in virus membranes.
    46   1. be able to map volume gray levels onto curved membrane surfaces
    47   1. move membrane surface along normals while viewing gray levels
    48   1. place markers on surfaces
    49   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
     44=== Core 2 (Higher order structure) ===
     45 1. Electron tomography: Visualization of objects embedded in membranes e.g. nuclear pores in nuclear envelope, spikes in virus membranes. Ticket #7181
     46  1. be able to map volume gray levels onto curved membrane surfaces Ticket #7182
     47  1. move membrane surface along normals while viewing gray levels Ticket #7183
     48  1. place markers on surfaces Ticket #7184
     49  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
    5050
    51 === Core 4 ===
    52  1. allow specifying "sequence to add" by accession code (Uniprot?). Its feature annotations would automatically come along as regions.  ECM
     51=== Core 4 (Sequence/Structure) ===
     52 1. allow specifying "sequence to add" by accession code (Uniprot?). Its feature annotations would automatically come along as regions.  Ticket #7186
    5353  * would we want Fetch by ID for sequences? (would we want a sequence with no structure and not aligned with any other sequences?)
    5454  * 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)
    5555  * on my secondary MAV to-do list. EFP
    56  1. When aligning in a structure sequence, consider secondary structure markups of non-structure sequences
    57  1. If gaps are created while adding a sequence, make corresponding gaps in any markups
    58  1. Aqua background -> gray, or put black border around sequence-name color swatches
     56 1. When aligning in a structure sequence, consider secondary structure markups of non-structure sequences Ticket #7187
     57 1. If gaps are created while adding a sequence, make corresponding gaps in any markups Ticket #7188
     58 1. Aqua background -> gray, or put black border around sequence-name color swatches Ticket #7189
    5959
    6060