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Build a structure in centroid from a blueprint given an input pdb.
<BluePrintBDR name="bdr" blueprint="input.blueprint" use_abego_bias="0" use_sequence_bias="0" scorefxn="scorefxn1"/>Options (default):
num_fragpick ( 200 ),
use_sequence_bias ( false ), use sequence bias in fragment picking
use_abego_bias ( false ), use abego bias in fragment picking
max_linear_chainbreak ( 0.07 ),
ss_from_blueprint ( true ),
constraints_NtoC ( -1.0 ),
constraints_sheet ( -1.0 ),
constraint_file ( "" ),
dump_pdb_when_fail ( "" ),
rmdl_attempts ( 1 ),
use_poly_val ( true ),
tell_vlb_to_not_touch_fold_tree (false),
invrot_tree_(NULL),
enzcst_io_(NULL)
Blueprint format:
resnum residue (ss_struct)(abego) rebuild
resnum = consecutive (starting from 1) or 0 (to indicate a new residue not in the input.pdb)
residue = one letter code amino acid (e.g. V for Valine)
ss_struct = secondary structure, E,L or H. ss_struct and abego are single-letter and have no space between them.
abego = abego type (ABEGO), use X if any is allowed
rebuild = R (rebuild this position) or "." (leave as is)
Examples
1 V LE R (position 1, Val, loop, abego type E, rebuild)
0 V EX R (insert a residue, Val, sheet, any abego, rebuild)
2 V EB . (position 2, Val, sheet, abego type B, do not rebuild)
Note that this is often used with a SetSecStructEnergies mover, which would be applied first, both calling the same blueprint file with a header indicating the desired pairing. See SetSecStructEnergiesMover for more.