[Jalview-discuss] secondary structure annotation

[Daron Standley]

Hi-

I am getting strange results for my secondary structure in a pairwise  
alignment using the jalview applet:

http://pdbjc01.protein.osaka-u.ac.jp:8888/tmp/ 
SS32349/3bknmodA_PDP_A_1jgcC_SCOP_A_applet.html

The secondary structure is supposed to correspond to the first  
sequence, which is passed to the applet as

<param name="sequence1" value="3bknmodA -------- 
NYILRAVFLESVASIPGLVHLRCLRRLQPDSWIKPLVD- 
AENERMHLLAVVQKLFIRITQFSFVTLFSFLFVFAPRTSHRLVGFLEEHAVDSYTEMIRRIDSNEDATLRDA 
LLVIRADEADHRLVNHSLGDAYDKKTPVSVK">

What is strange is that there is a helix where there are no 3bknmodA  
residues (e.g., in the N-terminal gap).
The secondary structure assignment is specified in an annotations  
file with the 3bknmodA sequence provided as the reference:

JALVIEW_ANNOTATION
SEQUENCE_REF	3bknmodA
BAR_GRAPH	Score	 0.06| 3.33| 1.68|-3.97|-1.44| 5.15|  
0.97|-3.17|-3.01| 6.67|-3.19| 0.22|  
5.66|-2.99|-3.08|-1.60|-4.00|-1.35| 4.88| 9.29| 0.86|  
6.61|-1.60|-2.18| 0.11|-1.57|-1.47|-2.34|-3.20|-2.28|  
0.09|-1.60|-1.56| 5.89|-1.59|-2.96|-3.17| 1.69| 2.06|-3.85| 0.03|  
6.65|-1.44|-3.19| 9.99|-1.51|-3.94|-0.64| 3.32| 3.31|-0.65| 2.48|  
1.83| 0.85| 0.00|-2.13|-4.00|-1.59| 0.86|-4.00| 0.91|  
1.06|-2.37|-0.70| 5.19|-3.97|-0.77| 0.86|-2.31| 0.03|-3.96|-3.98|  
0.01| 8.89| 6.64|-0.76| 1.61|-3.17|  
0.17|-1.51|-3.96|-4.00|-2.40|-3.56| 6.82| 0.14|-1.56| 5.34|  
0.94|-0.58|-3.01| 8.57|-1.53|  
4.76|-0.64|-2.53|-1.47|-2.39|-1.50|-2.27| 0.22|-3.11|-2.37|  
8.56|-1.51| 0.18|-3.10| 2.97| 2.12|-1.59| 1.55|-3.10|-1.57|  
2.37|-3.20| 0.27| 7.74| 6.53|-0.77|-1.42|  
9.90|-3.19|-3.98|-0.80|-4.00| 0.01| 1.75|-2.18|-4.79| 0.27|-1.50|  
8.03| 7.46| 2.78|-3.20|-1.56| 8.82|-2.40| 0.00|-0.80|-0.80|0|0|0|0|0| 
0|0|0|0|0|
NO_GRAPH	Secondary Structure	H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H| 
H|H|H|H|H|H|H|||H|H|H|H|H|||||H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H| 
H|||||||||||||||||||H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H| 
H|H|H|H|||H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H| 
H||H|H|H|H|H|H|H|H||||||||

I thought I had all of this secondary structure stuff sorted out, but  
obviously not. Can someone tell me what I am doing wrong?

Best wishes,

Daron 
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