Changes between Version 66 and Version 67 of Release1.4

Timestamp:

Dec 2, 2008, 11:45:00 AM (17 years ago)

Author:

Scooter Morris

Comment:

--

Release1.4

@@ -18 +18 @@
  1. Need "effects" command for controlling all Effects via script. ECM
  1. Reduce mmcif template file download
+ 1. Framework for invoking chimeraservices.rbvi.ucsf.edu and other web services CH
+  *  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. ECM
+    * (search other databases such as NR? PSI-BLAST on NR?)
 
 == Features Desired for 1.4 ==
@@ -24 +28 @@
   * Implement cron job to continuously update mmcif template file
 
+
 === Documentation ===
 
 === Core 2 ===
+ 1. 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
+  1. move membrane surface along normals while viewing gray levels
+  1. place markers on surfaces
+  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
 
 === Core 4 ===
+ 1. allow specifying "sequence to add" by accession code (Uniprot?). Its feature annotations would automatically come along as regions.  ECM
+  * 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
+ 1. If gaps are created while adding a sequence, make corresponding gaps in any markups
+ 1. Aqua background -> gray, or put black border around sequence-name color swatches
+
 
 == Features Postponed to 1.5 ==
 We will re-evaluate these features for the 1.5 release, but we think they are likely to be included.
  1. Implement mmcif template web service to update templates dynamically from chimera
+ 1. Allow sending template structure and template/target sequence alignment to comparative modeling program, either local or Web. ECM
+  * This will require discussion/clarification between Andre and Tom to align the research goals of the two groups
 
 == Features Postponed to 1.5+ ==