Changes between Initial Version and Version 1 of CoreFeatures

Timestamp:

Dec 24, 2008, 10:46:34 AM (17 years ago)

Author:

Scooter Morris

Comment:

--

CoreFeatures

@@ +1 @@
+== Possible Core Features for a Future Chimera Release ==
+
+ 1. Pull mmcif connectivity information from a web service.  The current mmcif connectivity template file is 20MB uncompressed and constantly out of date.  Rather than including the file in our release, the proposal is to include only the most common entries and pull the rest from a web service, as needed.  Entries will be cached once they are downloaded, and the user will be able to download the entire file, should they desire.
+ 1. CMS Surface code.
+ 1. 64-bit Mac Aqua build for large volume data applications. TG
+  * We had discussed having this happen when OS X 10.6 (Snow Leopard) comes out.  It's supposedly slated for Q1 2009. EFP
+ 1. Higher quality lighting and transparency using OpenGL shaders. TG
+    * I guess these would be options in the Effects panel; need "effects" command for controlling all Effects (not just these new things) via script. ECM
+ 1. Off-screen image saving (using opengl write-to-texture?) so machine does not become unusable during animation encoding. TG
+ 1. Replace mac aqua focus-follows-mouse with click-through. Tk patch probably required. TG
+ 1. ''Record usage statistics, submit with registration. TG''
+ 1. Output compressed TIFF instead of current giant files. ECM
+ 1. Color tint/fade capability (modulate instead of replacing current colors). ECM
+ 1. Provide our own Web services for BLAST on PDB, multiple sequence alignment (ties in with Core 4). ECM
+ 1. Interface with comparative modeling software (ties in with Core 4). ECM
+ 1. BILD and/or shape command ability to create ellipsoids.  ECM
+ 1. Nucleotides: saved in sessions, dialog settings maybe sticky, "nucleotides" command, possibly use in preset. ECM
+ 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
+ 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. ECM
+ 1. Minimize Structure: don't call Dock Prep again if all atoms already have amberType and topology has not changed. ECM
+ 1. Read PDBPQR format and load charge and radius values as the respective attributes. ECM
+   * Perhaps write PDBPQR format.
+   * Perhaps read PDBQT (Autodock format) and load charge, autodockType (or something like that).
+ 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
+ 1. Reposition normal labels with mouse. EFP
+ 1. ''Display multiple trajectory frames simultaneously. EFP''
+ 1. ''Trajectory smoothing. EFP''
+ 1. ''Trajectory analysis timeline plots. EFP''
+ 1. EMANimator++ EFP
+ 1. Tool configuration wizard. EFP
+ 1. Display preset wizard. EFP
+ 1. (planned/probable) Measure planes/centroids. EFP
+ 1. (planned/probable) Rename models using Model Panel. EFP
+ 1. (planned/probable) Coulombic surface coloring. EFP
+  * Elaine would like it to generate a map.
+ 1. (planned/probable) Finish Color Key (X3D output [needed for raytracing]; "key" option to rangecolor command). EFP
+ 1. integrate Nucleotides GC
+  * session support, command line, rings filling per residue, ''2D representation'', interpolating ribbons GC
+ 1. move Molecule color to Model GC
+ 1. Python 2.6 GC
+  * wrappy changes
+  * allows for 64-bit Windows builds (needs Microsoft Visual Studio 2008)
+ 1. off-screen rendering GC
+  * improve shadow resolution GC
+ 1. Improve VRML by making nodes into Python objects and selectable geometry GC
+ 1. ''X3D import GC''
+ 1. ''NURB ribbons GC''
+ 1. Bring OSMesa version to production status GC
+  * split test suite into gui and non-gui parts
+  * add tutorial
+ 1. Benchmark graphics options (multisampling, bgopacity) GC
+ 1. ''Support additional fonts GC''
+ 1. Add more types of dashed lines in POV-Ray/Renderman GC
+ 1. N-level transparency without sorting using depth-peeling GC
+ 1. ''Web update without reinstall CH''
+ 1. Web distribution of extensions CH
+ 1. Framework for invoking chimeraservices.rbvi.ucsf.edu CH
+  *  Security, transactions with IDs
+ 1. Animation interface (same as EMANimator++?) CH
+ 1. ''General grouping mechanism for domains, quaternary structures, regions, etc. (probably not for 1.4)''