Changes between Version 17 and Version 18 of HIVspikes

Timestamp:

Oct 8, 2009, 2:00:29 PM (17 years ago)

Author:

meng

Comment:

--

HIVspikes

@@ -127 +127 @@
 == Alternative from Elaine for glycosylation part ==
 
-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 can then be highlighted on both sequences.
+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.
 
-Say 1gc1 chain G (HIV gp120) is already open as model 0, 3fus (glycosylated SIV gp120) as model 1.  Then you could focus on the SIV structure (e.g. focus #1) and show the glycosylation (alias glyco #1 & ~ protein; show glyco).  Then discuss 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:
+Say 1gc1 chain G (HIV gp120) is already open as model 0, 3fus (glycosylated SIV gp120) as model 1. You could focus on the SIV structure (e.g. focus #1) and show the glycosylation:
+
+alias glyco #1 & ~ protein; show glyco
+
+Then discuss glycosylation. May want show attached Asn residues (disp #1:asn & glyco z<4) or fill sugar rings (fillring glyco).  Then superimpose the structures and show the pairwise sequence alignment:
 
 mm #1 #0 show true
 
+If the display is too busy, could hide the atoms at some point (~disp).  
+
 [[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. 
+The orange boxes on the sequence alignment are the parts used in the final fit and coincide with low values of the RMSD header, which in the pairwise case are simply CA-CA distances.  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.
+Edit... Find PROSITE Pattern N-x-[ST] reveals commonalities and differences.
 
 [[Image(pairMAV2.png)]] 
 
-Other things that could be done here:
+Other things that could be done include selecting the consensus sites, showing mavRMSD as worm on one structure, etc.
 
 == Cytoscape ==