63c63
< Include T0240.t2k.undertaker-align.under 
---
> # Include T0240.t2k.undertaker-align.under 
65c65
< ReadFragmentAlignment NOFILTER all-align.a2m
---
> 
69,70c69,72
< // InfilePrefix 1xxxX/
< //   include read-alignments.under
---
> InfilePrefix 1tolA/
>    include read-alignments-scwrl.under
> InfilePrefix 1lr0A/
>    include read-alignments-scwrl.under   
80c82
< TryAllAlign shrink 0.6 min_keep_length 1 
---
> TryAllAlign shrink 0.6 min_keep_length 1 cumulative
85c87
< TryAllAlign shrink 0.2 min_keep_length 1
---
> TryAllAlign shrink 0.2 min_keep_length 1 cumulative
88c90
< TryAllAlign shrink 0.3 min_keep_length 1
---
> TryAllAlign shrink 0.3 min_keep_length 1  cumulative
93c95
< TryAllAlign shrink 0.5 min_keep_length 1 
---
> TryAllAlign shrink 0.5 min_keep_length 1  cumulative
97a100,102
> SCWRLConform
> NameConform T0240.try5
> 
104c109
< ReadConformPDB /projects/compbio/data/pdb/1tol.pdb.gz
---
> 
114a120,121
> ReadFragmentAlignment T0240.t04.many.frag
> ReadFragmentAlignment NOFILTER all-align.a2m
147,149d153
< # SCWRLConform
< NameConform T0240.try5
<