Changes between Version 14 and Version 15 of HIVspikes

Timestamp:

Oct 8, 2009, 1:45:21 PM (17 years ago)

Author:

meng

Comment:

--

HIVspikes

@@ -125 +125 @@
 to see the dense coverage by sugars.
 
+== Alternative from Elaine for glycosylation stuff... ==
+
+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 also indicated with the RMSD header, and consensus glycosylation sites can then be highlighted on both sequences. This is sort of the opposite ordering as what you had above.
+
+Details...
+Say 1gc1 chain G (HIV gp120) is already open as model 0, 3fus (glycosylated SIV gp120) as model 1.  Then the following could be done:
+
+focus #1
+alias glyco #1 & ~ protein
+show glyco
+
+Then talk about glycosylation. May want show attached Asn residues (disp #1:asn & glyco z<4) or fill sugar rings (fillring glyco) or just hide all the atoms (~disp).  Then superimpose the structures and show the pairwise sequence alignment:
+
+mm #1 #0 show true
+
+[[Image(pairmatch.png)]] [[Image(pairmatchglyco.png)]]
+
+The orange boxes on the sequence alignment are the parts used in the final fit and coincide with low values of the RMSD header (in pairwise case collapses to simply CA-CA distance).  Clicking the orange region selects the corresponding parts of the structures. 
+
+[[Image(pairMAV1.png)]]
+
+Edit... Find PROSITE Pattern N-x-[ST] on both sequences reveals commonalities and differences.
+
+[[Image(pairMAV2.png)]] 
+
+Other things that could be done here:
+
 == Cytoscape ==