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I've tried to use the cyclic symmetric mode to generate a set of symmetric loops between symmetric structural units (e.g. loops to join together helices in a helical bundle with cyclic symmetry).
However, while this kind of operation works to generate non-symmetric loops, when switching to use of symmetry it acts to always assume chain-breaks after the newly generated loops, such that they are never positioned so as to actually join the e.g. helices of the symmetric helical bundle.
Based on the text in the nickel design example, which says that chain breaks don't strictly need to be given in the contigs when using symmetry, it seems this might be a known limitation of the symmetry mode. Is this true?
Is it possible to circumvent this limitation? I see at a broad level why using symmetry to generate a symmetric monomer could prove a difficulty in regions where a backbone frame from one symmetry group needed to contact a frame from another group and both were being diffused, but maybe in the case of the contacts being between fixed regions it is not so problematic?
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I've tried to use the cyclic symmetric mode to generate a set of symmetric loops between symmetric structural units (e.g. loops to join together helices in a helical bundle with cyclic symmetry).
However, while this kind of operation works to generate non-symmetric loops, when switching to use of symmetry it acts to always assume chain-breaks after the newly generated loops, such that they are never positioned so as to actually join the e.g. helices of the symmetric helical bundle.
Based on the text in the nickel design example, which says that chain breaks don't strictly need to be given in the contigs when using symmetry, it seems this might be a known limitation of the symmetry mode. Is this true?
Is it possible to circumvent this limitation? I see at a broad level why using symmetry to generate a symmetric monomer could prove a difficulty in regions where a backbone frame from one symmetry group needed to contact a frame from another group and both were being diffused, but maybe in the case of the contacts being between fixed regions it is not so problematic?
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