X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2FscoreModel%2Fpam250.scm;h=898c723bbf7a8855270f2126aaec112135982e0e;hb=c793942b6430bba9d9b6795e4afd8a1907c022d7;hp=05404d0654c6f5d82093a593bf28f27b271b6980;hpb=613a7a5d1fe2758f0bb620e49eeb87fa45b5458f;p=jalview.git

diff --git a/resources/scoreModel/pam250.scm b/resources/scoreModel/pam250.scm
index 05404d0..898c723 100644
--- a/resources/scoreModel/pam250.scm
+++ b/resources/scoreModel/pam250.scm
@@ -1,36 +1,32 @@
 ScoreMatrix PAM250
-ARNDCQEGHILKMFPSTWYVBZX-*
 #
 # The PAM250 substitution matrix
 # The first line declares a ScoreMatrix with the name PAM250 (shown in menus)
 # Scores are not case sensitive, unless column(s) are provided for lower case characters
 # Values may be integer or floating point, delimited by tab, space, comma or combinations
 #
-#	A	R	N	D	C	Q	E	G	H	I	L	K	M	F	P	S	T	W	Y	V	B	Z	X	-	*
-A	2	-2	0	0	-2	0	0	1	-1	-1	-2	-1	-1	-3	1	1	1	-6	-3	0	0	0	0	-8	-8
-R	-2	6	0	-1	-4	1	-1	-3	2	-2	-3	3	0	-4	0	0	-1	2	-4	-2	-1	0	-1	-8	-8
-N	0	0	2	2	-4	1	1	0	2	-2	-3	1	-2	-3	0	1	0	-4	-2	-2	2	1	0	-8	-8
-D	0	-1	2	4	-5	2	3	1	1	-2	-4	0	-3	-6	-1	0	0	-7	-4	-2	3	3	-1	-8	-8
-C	-2	-4	-4	-5	12	-5	-5	-3	-3	-2	-6	-5	-5	-4	-3	0	-2	-8	0	-2	-4	-5	-3	-8	-8	
-Q	0	1	1	2	-5	4	2	-1	3	-2	-2	1	-1	-5	0	-1	-1	-5	-4	-2	1	3	-1	-8	-8	
-E	0	-1	1	3	-5	2	4	0	1	-2	-3	0	-2	-5	-1	0	0	-7	-4	-2	3	3	-1	-8	-8	
-G	1	-3	0	1	-3	-1	0	5	-2	-3	-4	-2	-3	-5	0	1	0	-7	-5	-1	0	0	-1	-8	-8	
-H	-1	2	2	1	-3	3	1	-2	6	-2	-2	0	-2	-2	0	-1	-1	-3	0	-2	1	2	-1	-8	-8	
-I	-1	-2	-2	-2	-2	-2	-2	-3	-2	5	2	-2	2	1	-2	-1	0	-5	-1	4	-2	-2	-1	-8	-8	
-L	-2	-3	-3	-4	-6	-2	-3	-4	-2	2	6	-3	4	2	-3	-3	-2	-2	-1	2	-3	-3	-1	-8	-8	
-K	-1	3	1	0	-5	1	0	-2	0	-2	-3	5	0	-5	-1	0	0	-3	-4	-2	1	0	-1	-8	-8	
-M	-1	0	-2	-3	-5	-1	-2	-3	-2	2	4	0	6	0	-2	-2	-1	-4	-2	2	-2	-2	-1	-8	-8	
-F	-3	-4	-3	-6	-4	-5	-5	-5	-2	1	2	-5	0	9	-5	-3	-3	0	7	-1	-4	-5	-2	-8	-8	
-P	1	0	0	-1	-3	0	-1	0	0	-2	-3	-1	-2	-5	6	1	0	-6	-5	-1	-1	0	-1	-8	-8	
-S	1	0	1	0	0	-1	0	1	-1	-1	-3	0	-2	-3	1	2	1	-2	-3	-1	0	0	 0	-8	-8	
-T	1	-1	0	0	-2	-1	0	0	-1	0	-2	0	-1	-3	0	1	3	-5	-3	0	0	-1	 0	-8	-8	
-W	-6	2	-4	-7	-8	-5	-7	-7	-3	-5	-2	-3	-4	0	-6	-2	-5	17	0	-6	-5	-6	-4	-8	-8	
-Y	-3	-4	-2	-4	0	-4	-4	-5	0	-1	-1	-4	-2	7	-5	-3	-3	0	10	-2	-3	-4	-2	-8	-8	
-V	0	-2	-2	-2	-2	-2	-2	-1	-2	4	2	-2	2	-1	-1	-1	0	-6	-2	4	-2	-2	-1	-8	-8	
-B	0	-1	2	3	-4	1	3	0	1	-2	-3	1	-2	-4	-1	0	0	-5	-3	-2	3	2	-1	-8	-8	
-Z	0	0	1	3	-5	3	3	0	2	-2	-3	0	-2	-5	0	0	-1	-6	-4	-2	2	3	-1	-8	-8	
-X	0	-1	0	-1	-3	-1	-1	-1	-1	-1	-1	-1	-1	-2	-1	0	0	-4	-2	-1	-1	-1	-1	-8	-8	
--	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	 1   1
-*	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	 1   1
-#
-#	A	R	N	D	C	Q	E	G	H	I	L	K	M	F	P	S	T	W	Y	V	B	Z	X	*
+	 A	 R	 N	 D	 C	 Q	 E	 G	 H	 I	 L	 K	 M	 F	 P	 S	 T	 W	 Y	 V	 B	 Z	 X	 *
+A	 2	-2	 0	 0	-2	 0	 0	 1	-1	-1	-2	-1	-1	-3	 1	 1	 1	-6	-3	 0	 0	 0	 0	-8
+R	-2	 6	 0	-1	-4	 1	-1	-3	 2	-2	-3	 3	 0	-4	 0	 0	-1	 2	-4	-2	-1	 0	-1	-8
+N	 0	 0	 2	 2	-4	 1	 1	 0	 2	-2	-3	 1	-2	-3	 0	 1	 0	-4	-2	-2	 2	 1	 0	-8
+D	 0	-1	 2	 4	-5	 2	 3	 1	 1	-2	-4	 0	-3	-6	-1	 0	 0	-7	-4	-2	 3	 3	-1	-8
+C	-2	-4	-4	-5	12	-5	-5	-3	-3	-2	-6	-5	-5	-4	-3	 0	-2	-8	 0	-2	-4	-5	-3	-8
+Q	 0	 1	 1	 2	-5	 4	 2	-1	 3	-2	-2	 1	-1	-5	 0	-1	-1	-5	-4	-2	 1	 3	-1	-8
+E	 0	-1	 1	 3	-5	 2	 4	 0	 1	-2	-3	 0	-2	-5	-1	 0	 0	-7	-4	-2	 3	 3	-1	-8
+G	 1	-3	 0	 1	-3	-1	 0	 5	-2	-3	-4	-2	-3	-5	 0	 1	 0	-7	-5	-1	 0	 0	-1	-8
+H	-1	 2	 2	 1	-3	 3	 1	-2	 6	-2	-2	 0	-2	-2	 0	-1	-1	-3	 0	-2	 1	 2	-1	-8
+I	-1	-2	-2	-2	-2	-2	-2	-3	-2	 5	 2	-2	 2	 1	-2	-1	 0	-5	-1	 4	-2	-2	-1	-8
+L	-2	-3	-3	-4	-6	-2	-3	-4	-2	 2	 6	-3	 4	 2	-3	-3	-2	-2	-1	 2	-3	-3	-1	-8
+K	-1	 3	 1	 0	-5	 1	 0	-2	 0	-2	-3	 5	 0	-5	-1	 0	 0	-3	-4	-2	 1	 0	-1	-8
+M	-1	 0	-2	-3	-5	-1	-2	-3	-2	 2	 4	 0	 6	 0	-2	-2	-1	-4	-2	 2	-2	-2	-1	-8
+F	-3	-4	-3	-6	-4	-5	-5	-5	-2	 1	 2	-5	 0	9	-5	-3	-3	 0	 7	-1	-4	-5	-2	-8
+P	 1	 0	 0	-1	-3	 0	-1	 0	 0	-2	-3	-1	-2	-5	 6	 1	 0	-6	-5	-1	-1	 0	-1	-8
+S	 1	 0	 1	 0	 0	-1	 0	 1	-1	-1	-3	 0	-2	-3	 1	 2	 1	-2	-3	-1	 0	 0	 0	-8
+T	 1	-1	 0	 0	-2	-1	 0	 0	-1	 0	-2	 0	-1	-3	 0	 1	 3	-5	-3	 0	 0	-1	 0	-8
+W	-6	 2	-4	-7	-8	-5	-7	-7	-3	-5	-2	-3	-4	 0	-6	-2	-5	17	 0	-6	-5	-6	-4	-8
+Y	-3	-4	-2	-4	 0	-4	-4	-5	 0	-1	-1	-4	-2	 7	-5	-3	-3	 0	10	-2	-3	-4	-2	-8
+V	 0	-2	-2	-2	-2	-2	-2	-1	-2	 4	 2	-2	 2	-1	-1	-1	 0	-6	-2	 4	-2	-2	-1	-8
+B	 0	-1	 2	 3	-4	 1	 3	 0	 1	-2	-3	 1	-2	-4	-1	 0	 0	-5	-3	-2	 3	 2	-1	-8
+Z	 0	 0	 1	 3	-5	 3	 3	 0	 2	-2	-3	 0	-2	-5	 0	 0	-1	-6	-4	-2	 2	 3	-1	-8
+X	 0	-1	 0	-1	-3	-1	-1	-1	-1	-1	-1	-1	-1	-2	-1	 0	 0	-4	-2	-1	-1	-1	-1	-8
+*	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	-8	 1