Changes between Version 20 and Version 21 of HIVspikes

Timestamp:

Oct 8, 2009, 2:59:40 PM (17 years ago)

Author:

meng

Comment:

--

HIVspikes

@@ -125 +125 @@
 to see the dense coverage by sugars.
 
-== Alternative from Elaine for glycosylation part ==
+== Glycosylation alternative (Elaine) ==
 
 Instead of showing glycosylation consensus sites on the single sequence, you could use Matchmaker to superimpose HIV1 gp120 and glycosylated SIV gp120 and show the corresponding pairwise sequence alignment.  Regions that superimpose well are automatically highlighted with orange boxes, and consensus glycosylation sites could then be highlighted on both sequences.
@@ -154 +154 @@
 
 Another possibility here is calculating percent ID (Tools... Percent Identity).
+
+== Conservation alternative (Elaine) ==
+
+Could color the gp120 structure by conservation, showing that the antibody and CD4 in structure 1gc1 are interacting with fairly well-conserved regions of gp120.
+
+Open 1gc1 and the alignment pdb1gc1.aln (attached).  Ahead of time, use Multalign Viewer Preferences... Headers to change Conservation style to AL2CO (otherwise default). Then use Structure... Render by Conservation and adjust settings as shown in the Render dialog (lowest or most variable red, highest or most conserved blue, no-value residues gray).
+
+[[Image(colorcons.png)]] [[Image(render-cons.png)]]
+
+The gray segment in gp120 is where the alignment column had too few sequences (too many gaps) to calculate a reliable conservation value.  Clearly the interfaces are not at the reddest, most variable surface of the gp120 core structure.
 
 == Cytoscape ==