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BridgeChains mover deletes residues at break

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BridgeChains mover deletes residues at break

I'm trying to use the BridgeChains mover in Rosettascripts to build a linker between two domains as described in Kuhlman et al 2016. As a test case, I'm just building a missing 7 residue loop in the A chain of 1Z92 using the basic protocol described in the BridgeChains documentation. I've created a pdb file that includes just the A chain, renumbered to begin at residue 1, with a TER line inserted at the break; the chain break between residues 68 and 76 looks like this:

ATOM    562  CB  ALA A  68      -4.007 -39.491   3.888  1.00 66.55      A    C
ATOM    563  N   ARG A  76      -8.535 -44.152  -3.863  1.00 60.86      A    N

I then run rosetta_scripts using a basic xml script to build a 7 residue loop:

        <ScoreFunction name="centroid_scorefunction" weights="fldsgn_cen"/>
        <BridgeChains name="connect" chain1="1" chain2="2" motif="7LX" overlap="0" scorefxn="centroid_scorefunction" />
        <Add mover_name="connect"/>

I expect this to build a 7-residue poly-Val linker between residues 68 and 76, but for reasons I don't understand, the output structures are missing the C-terminal Ala68  of chain 1 and the N-terminal Arg76 of chain 2, with a new 7-residue linker bridging the old residues 67-77. Any help in understanding this behavior would be much appreciated.



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Thu, 2024-02-22 12:14