The tutorial at https://www.rosettacommons.org/demos/latest/tutorials/loop_modeling/loop_modeling says "You can build multiple loops in the same simulation by altering the blueprint file to indicate where these loops are".
I have a blueprint like below with 3 fragments to insert (at the end of this post). It can be run without errors, but all the inserted residues are VAL. Only when I insert one fragment at a time, the newly built residues are correct.
Can I ask is this something I did incorrectly, or is it the bug of the protocol?
Flag:
-in:file:s protein.pdb
-remodel:blueprint protein.remodel
-remodel:num_trajectory 1
-remodel:quick_and_dirty
-out:path:all output_files
-out:file:scorefile protein.sc
-chain A
Blueprint:
(omit)
97 A .
98 P .
99 T .
100 T L PIKAA T
0 X L PIKAA V
101 V L PIKAA V
102 P .
103 F .
104 A .
(omit)
127 L .
128 A .
129 P .
130 S L PIKAA S
0 X L PIKAA S
0 X L PIKAA K
0 X L PIKAA S
0 X L PIKAA T
0 X L PIKAA S
0 X L PIKAA G
131 G L PIKAA G
132 T .
133 A .
(omit)
206 K .
207 K .
208 V .
209 E .
210 P L PIKAA P
0 X L PIKAA K
0 X L PIKAA S
0 X L PIKAA C
0 X L PIKAA D