Changes between Version 13 and Version 14 of SiteVisit

Timestamp:

Aug 26, 2011, 11:38:06 AM (15 years ago)

Author:

meng

Comment:

--

SiteVisit

@@ -23 +23 @@
  * 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)
+ * other fetch by ID (EMDB, PubChem, ...) and caching
  * 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)
+ * superposition
+ * find clashes and/or H-bonds
  * 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?
@@ -47 +50 @@
  * [http://www.cgl.ucsf.edu/Research/auer/gut-sep2010/ Termite gut] - Segmentation tool demo.
  * [http://en.wikipedia.org/wiki/Myofibrils Muscle filaments], myosin / actin / tropomyosin.  Another good "composite" model example.  Haven't done much with this system yet though.  Recent Roger Craig / Raul Padron [http://www.ncbi.nlm.nih.gov/pubmed/21705660 paper], PNAS July 2011
- * influenza virus - electron tomography of viral particles; recently discovered broadly neutralizing Abs, crystal structures of these bound to hemagglutinin, Science 12 Aug 2011 issue; EM/fitting work on RNPs (the stuff inside the capsid)
+ * influenza virus - electron tomography of viral particles; recently discovered broadly neutralizing Abs, crystal structures of these bound to hemagglutinin, 2 papers and Perspective article in [http://www.sciencemag.org/content/333/6044.toc Science 12 Aug 2011 issue]; EM/fitting work on RNPs (the stuff inside the capsid)
 
 === TR&D 3 ===