Changes between Version 18 and Version 19 of HIVspikes

Timestamp:

Oct 8, 2009, 2:12:18 PM (17 years ago)

Author:

meng

Comment:

--

HIVspikes

@@ -129 +129 @@
 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. You could focus on the SIV structure (e.g. focus #1) and show the glycosylation:
+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 and show the glycosylation:
 
-alias glyco #1 & ~ protein; show glyco
+focus #1
+
+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:
@@ -139 +143 @@
 If the display is too busy, could hide the atoms at some point (~disp).  
 
-[[Image(pairmatch.png)]] [[Image(pairmatchglyco.png)]]
+[[Image(pairmatchglyco.png)]] [[Image(pairmatch.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, which in the pairwise case are simply CA-CA distances.  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 iteration and coincide with low values of the RMSD header, which in the pairwise case collapses to CA-CA distance per alignment column.  Clicking the orange region selects the corresponding parts of the structures. 
 
 [[Image(pairMAV1.png)]]
@@ -149 +153 @@
 [[Image(pairMAV2.png)]] 
 
-Other things that could be done include selecting the consensus sites, showing mavRMSD as worm on one structure, etc.
+Another possibility here is calculating percent ID (Tools... Percent Identity).
 
 == Cytoscape ==