Changes between Version 11 and Version 12 of SiteVisit

Timestamp:

Aug 26, 2011, 11:14:52 AM (15 years ago)

Author:

meng

Comment:

--

SiteVisit

@@ -15 +15 @@
  * BLAST service
  * Modeller interface
- * multiple alignment from source other than BLAST if we want to make statements about conservation, perhaps with corresponding tree (domain family seed alignments + trees can be obtained from Pfam)
- * multiple alignment Conservation header (sequence conservation, AL2CO options include entropy, variability, etc.)
- * multiple alignment RMSD header (spatial conservation of associated superimposed structures)
+ * useful chain information now appears in status upon mouseover in graphics window
+ * multiple alignment from source other than BLAST if we want to make statements about conservation, perhaps with corresponding tree (for example, domain family seed alignments + trees can be obtained from Pfam; for 2009 we got seqs from HIV database)
+ * alignment Conservation header (sequence conservation, AL2CO options include entropy, variability, etc.)
+ * alignment RMSD header (spatial conservation of associated superimposed structures)
+ * custom header (used in 2009 hivspikes demo to show importance for antibody binding, probably not time for it this year)
  * render by attribute (could be attribute from MAV header or other such as bfactor or Modeller error profile)
  * Uniprot annotations on sequence either from direct Uniprot fetch of sequence or from using PDB/UniProt Info tool
  (good for showing relationship of gp120 core constructs in which loops had been replaced with stubs to the full-length sequence... unfortunately PDB SIFTS service has a data problem with 1GC1 but 1GM9 is nearly identical and could be used instead)
+ * a time-saving suggestion is to put aliases in a startup (.midasrc) file, then without having to use a previously saved session it is easy to do something to predefined sets of residues, e.g. "color red epitope1"
+ * ProfileGrid (existing standalone, allows presenting some future plans; downside is that it is probably hard to see and understand up on a projected screen)
+ * morphing was shown last site visit
+ * flying through positions or scenes?  are we going to do anything about presentation tools other than Tom's web log?
 
 === TR&D 2 ===