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Remodel introduces clashes when stitching

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Remodel introduces clashes when stitching

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 -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

model3_0001.png426.93 KB
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Thu, 2016-08-25 17:51

It is not clear to me from the picture where the red helix is to be connected to on the side the clashes.  Because all the splicing and joining and using fragments to bridge the links are done at the centroid level -- and driven by increasing restraints to force the chains to be closed, it is possible that you will get clashes, if the inserted piece does not have proper flexibility or proper number of flanking residues.    Additionally, your result is from a single trajectory, and that is sometimes limiting in trying to resolve a complex topology (even though in this case it seems simple).   If you need more help please email me the blueprint and pdb file (possu at, and I can hopefully give you suggestions.  best, possu 

Tue, 2016-08-30 16:57