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Can I use next generation KIC with fragments?

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Can I use next generation KIC with fragments?


I have a question about KIC protocol. I am using the next generation protocol together with fragments. I think it should be fine but I just wanted ti double check couple of things.

Firstly, can I use fragments together with these flags? :


I am just checking that there isnt some kind of "conflict of interest" between using these flags as well as the fragments.


Secondly, the flag -loops:fix_natsc, does it just stop Rosetta remodelling the side chains of neigbouring residues? Not the actual loop residues?


And finally, when I am generating fragments, am I suppose to submit the full protein seqeuence to the Robetta or just the residues that are found within the loops?


Thank you so much! I am really gratefull for your help


My full flas file:


-nstruct 500
-loops:remodel perturb_kic_with_fragments
-loops:refine refine_kic_with_fragments
-rebuild_disulf true
#-in:detect_disulf true
-loops:loop_file 4MWF.loops
-constraints:cst_fa_file 4MWF.fa.cst
-constraints:cst_fa_weight 20.0
-constraints:cst_file 4MWF.cst
-constraints:cst_weight 20.0
#-in:fix_disulf 4MWF.disulf.txt
#-packing:resfile 4MWF.resfile
-loops:frag_sizes 9 3 1
-loops:frag_files  /d/as12/u/sl002/rosett/run/loop/run_1/9mers.txt /d/as12/u/sl002/rosett/run/loop/run_1/3mers.txt none



Thank you



Post Situation: 
Thu, 2017-12-07 06:19

Can anybody help?

Wed, 2017-12-13 05:27