Changes between Version 67 and Version 68 of Release1.4


Ignore:
Timestamp:
Dec 2, 2008, 12:27:45 PM (17 years ago)
Author:
Scooter Morris
Comment:

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  • Release1.4

    v67 v68  
    2121  *  Security, transactions with IDs
    2222 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?)
     23  * (search other databases such as NR? PSI-BLAST on NR?)
    2424
    2525== Features Desired for 1.4 ==
    … …  
    2727 1. Distribute smaller mmcif template file, but provide a location for users to download the full template file from our web site
    2828  * Implement cron job to continuously update mmcif template file
     29 1. Output compressed TIFF instead of current giant files. ECM
     30 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.
     31 1. Reposition normal labels with mouse. EFP
     32 1. (planned/probable) Finish Color Key (X3D output [needed for raytracing]; "key" option to rangecolor command). EFP
     33 1. integrate Nucleotides GC
     34  * interpolating ribbons GC
    2935
    3036
    3137=== Documentation ===
     38
     39 1. Need new image-making tutorial(s) in addition to or replacing the current one. ECM
    3240
    3341=== Core 2 ===
    … …  
    5361 1. Allow sending template structure and template/target sequence alignment to comparative modeling program, either local or Web. ECM
    5462  * This will require discussion/clarification between Andre and Tom to align the research goals of the two groups
     63 1. 64-bit Mac Aqua build for large volume data applications. TG
     64  * We had discussed having this happen when OS X 10.6 (Snow Leopard) comes out.  It's supposedly slated for Q1 2009. EFP
     65 1. Higher quality lighting and transparency using OpenGL shaders. TG
     66  * Maybe discussed in conjunction with a more complete discussion about improving scenegraphs
     67 1. Color tint/fade capability (modulate instead of replacing current colors). ECM
     68 1. MD Movie: checkbox in Per-Frame panel and/or Record Movie panel to recompute secondary structure (make it more obvious that ribbon display may need to be updated). ECM
     69 1. Read PDBPQR format and load charge and radius values as the respective attributes. ECM
     70   * Perhaps write PDBPQR format.
     71   * Perhaps read PDBQT (Autodock format) and load charge, autodockType (or something like that).
     72 1. Make it easier to get phi,psi,omega,chi torsion values from proteins.  Maybe a button on Angles/Torsions to assign the values as residue attributes?
     73   * Longer term, interactive Ramachandran plot.  ECM
     74 1. Display preset wizard. EFP
     75 1. Python 2.6 GC
     76  * wrappy changes
     77  * allows for 64-bit Windows builds (needs Microsoft Visual Studio 2008)
     78 1. Improve VRML by making nodes into Python objects and selectable geometry GC
     79 1. Bring OSMesa version to production status GC
     80  * split test suite into gui and non-gui parts
     81  * add tutorial
     82 1. Benchmark graphics options (multisampling, bgopacity) GC
     83 1. Add more types of dashed lines in POV-Ray/Renderman GC
     84 1. N-level transparency without sorting using depth-peeling GC
    5585
    5686== Features Postponed to 1.5+ ==
    5787These features will be re-evaluated for the 1.5 release, but we think they are likely to be postponed beyond that.
     88 1. EMANimator++ EFP
     89  * Tom and Wau will look for additional funding to support this
     90 1. Tool configuration wizard. EFP
    5891
    5992== Features Dropped ==
    … …  
    84117   * Perhaps write PDBPQR format.
    85118   * Perhaps read PDBQT (Autodock format) and load charge, autodockType (or something like that).
    86  1. Make it easier to get phi,psi,omega,chi torsion values from proteins.  Maybe a button on Angles/Torsions to assign the values as residue attributes?  Longer term, interactive Ramachandran plot.  ECM
     119 1. Make it easier to get phi,psi,omega,chi torsion values from proteins.  Maybe a button on Angles/Torsions to assign the values as residue attributes? 
     120   * Longer term, interactive Ramachandran plot.  ECM
    87121 1. Reposition normal labels with mouse. EFP
    88122 1. ''Display multiple trajectory frames simultaneously. EFP''