Kevin Karplus 10 May 1998 t48 is SW:PHS_PSEAE The claimed homology seems to be to 1dcha, which has fssp-24-4-98 representative 1dcpA (there are 24 identical chains in pdb: 8 each in 1dch, 1dco, 1dcp). The template models pick up only 1dchA and 1dcpA also, giving these an excellent score. There is not much point to building an fssp-based alignment, as the only siginificant structural homologs have 100% sequence identity. -------------------------------------------------- 11 May 1998 The global alignment 1dcpA-t48-global is gapless and has high residue identity. This is an alignment no one can miss---a pure homology modeling target. 25 July 1998 I'm going to remake everything with the newest Makefile, so I get decent 2ry structure prediction. I don't expect any new results. wu-blast finds 1dch[*] 1dco[*] 1dcp[*] (-16.6) and 2hntE (-5.878) double-blast the same. target model t48.t98_6 finds the same 1dc* (-116.53), but gets nothing else below -3.4 template models: 1dchA -93.09, 1dcpA -89.21 summed: 1dchA -209.62, 1dcpA -205.74 26 July 1998 best alignments: 1dchA/t48-1dchA-global 1dchA 99 -117.52 -121.13 1dchA/t48-1dchA-post 1dchA 99 -118.91 -121.13 1dcpA/t48-1dcpA-global 1dcpA 99 -117.52 -121.13 1dcpA/t48-1dcpA-post 1dcpA 99 -118.91 -121.13 1dchA/t48-1dchA-vit 1dchA 99 -116.51 -116.03 1dcpA/t48-1dcpA-vit 1dcpA 99 -116.51 -116.03 1dcpA/1dcpA-t48-global T0048 118 -90.99 -90.79 1dcpA/1dcpA-t48-post T0048 118 -92.38 -90.79 1dcpA/1dcpA-t48-const-global T0048 118 -88.03 -88.26 1dcpA/1dcpA-t48-fssp-global T0048 118 -85.84 -85.96 1dcpA/1dcpA-t48-vit T0048 118 -87.04 -84.96 Since 1dchA and 1dcpA are 100% identical at the residue level (in the fssp alignment), and they have only a 0.4 Angs RMS difference, there is not much need to choose between them. Let's pick 1dcpA, since that is what FSSP chose. Use the gapless alignment t48-1dcpA-global.