Hi all,
So I have been trying to stitch homology models together using Remodel and when it stitches the stitched piece often ends up clashing with the structure it is stitched onto. I am using the following command:
remodel.linuxgccrelease -s model3.pdb -remodel:domainFusion:insert_segment_from_pdb model4.pdb -remodel:blueprint model3.blueprint -use_input_sc -save_top 1 -overwrite -out:file:scorefile model3.sc -run:chain A >> model3.out
I am wondering if there is a way to align the attached segment to the part of the protein it is replacing or whether there is some way to prevent the the result seent in model3_0001