Changes between Version 25 and Version 26 of HIVspikes

Timestamp:

Oct 11, 2009, 9:54:55 AM (17 years ago)

Author:

meng

Comment:

--

HIVspikes

@@ -64 +64 @@
 doesn't let you specify a chain.  We don't want CD4 and other FAB structures, so first delete all
 but gp120 (chain G) then do the blast.
+(Elaine: alternatively, "split" beforehand if you would rather keep the other chains)
 
 [[Image(1gc1G_blast.png)]]
@@ -149 +150 @@
 [[Image(pairMAV1.png)]]
 
-Edit... Find PROSITE Pattern N-x-[ST] reveals commonalities and differences.
+Multalign Viewer menu Edit... Find PROSITE Pattern N-x-[ST] reveals commonalities and differences.
 
 [[Image(pairMAV2.png)]] 
 
-Another possibility here is calculating percent ID (in Multalign Viewer menu, Tools... Percent Identity).
+Alternatively, instead of finding the pattern on the sequence, just select it on the structures directly with main menu Select... Sequence, PROSITE Pattern, which is then reflected in the green selection region on the sequences (could "color yellow :asn & sel" or something like that). Another possibility here is calculating percent ID (in Multalign Viewer menu, Tools... Percent Identity).
 
 == Conservation alternative (Elaine) ==
@@ -165 +166 @@
 The gray segment in gp120 is where the alignment column had too few sequences (too many gaps) to calculate a reliable conservation value.  The redder, more variable parts of the gp120 core structure are not interacting with the other chains.
 
-Another possibility is using (main menu) Select... Sequence... gag to show where longer loops were replaced with gly-ala-gly to create this crystallizable gp120 core construct.
+Another possibility is using (main menu) Select... Sequence... gag to show where longer loops were replaced with gly-ala-gly to create this crystallizable gp120 core construct. Some other sequences in the alignment have the full-length loops.
 
 == Cytoscape ==