Changes between Version 12 and Version 13 of Release1.4

Timestamp:

Nov 24, 2008, 4:27:02 PM (17 years ago)

Author:

meng

Comment:

--

Release1.4

@@ -10 +10 @@
   * 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. Chimera Web service to BLAST on PDB  (NR database too? PSI-BLAST on NR?) ECM
- 1. Chimera Web service to multiple sequence alignment program (Muscle, T-Coffee, ... see [http://www.cgl.ucsf.edu/home/meng/sources.html#d list and links]) ECM
+ 1. connect to our own Web service to BLAST on PDB, provide dialog for choosing which hits to open, whether to show pairwise sequence alignment from BLAST (in MAV), whether to superimpose hit and query (with Matchmaker). ECM
+    * (NR database too? PSI-BLAST on NR?)
+ 1. connect to our own Web service to multiple sequence alignment program (Muscle, T-Coffee, ... see [http://www.cgl.ucsf.edu/home/meng/sources.html#d list and links]), show result in MAV. ECM
+ 1. Nucleotides saved in sessions, dialog settings sticky, "nucleotides" command, possibly used in preset. ECM
+ 1. MD Movie checkbox in Per-Frame 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
+
+==== Documentation ====
+
+ 1. Need new image-making tutorial(s) in addition to or replacing the current one. ECM
 
 === Project Related Features ===
@@ -71 +80 @@
 ==== Sequence/Structure (Core 4) ====
 
+ * send sequence alignment to multiple alignment Web server. ECM
+ * show sequence alignment returned by Web server (from BLAST on PDB, PSI-BLAST on NR, multiple alignment, etc.) ECM
+ * allow editing sequence name. ECM
+ * allow specifying sequence accession (Uniprot perhaps?) for annotation retrieval. ECM
+    a. send accession to Uniprot, get back XML with feature annotations, load them as sequence regions. ECM
+ * easier reporting of amino acid phi,psi,omega,chiN (perhaps this is Chimera core but one could imagine some connection to Multalign Viewer since it only applies to peptide/protein sequences). ECM
+
 ==== Other Projects ====