Loop modelling,

[Anonymous]

Hi,

I preform using loop modelling base of fragment database to remodel the loops of a protein,
But when it generates several models (e.g., 10000), it changes the other part of the protein (e.g., helix conformer) too.
But I expect , only remodels the loops site not other sites.

Thanks

[Anonymous]

Hi Berk,

Only thing I can think of is that something is strange with your loop file or input flags. Can you post both?

[Anonymous]

Hi,
Thanks,
Now my problem is solved , as I used this commands,
-loops:input_pdb inputs/Inactive_min_ph.pdb
-loops:loop_file inputs/Inactive.loop_file
-loops:frag_sizes 9 3 1
-loops:frag_files inputs/aat000_09_05.200_v1_3.gz inputs/aat000_09_05.200_v1_3.gz none
-loops:remodel quick_ccd
-loops:remodel perturb_kic
-loops:refine refine_kic
-loops:fix_natsc true
-loops:neighbor_dist 0.0
-loops:extended
-ex1
-ex2
-out:pdb
-out:prefix Inactive_H
-out:file:fullatom
-nstruct 1000

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