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Performs comparative modeling as described in detail in:
High-resolution comparative modeling with RosettaCM.
Song Y, DiMaio F, Wang RY, Kim D, Miles C, Brunette T, Thompson J, Baker D., Structure. 2013 Oct 8;21(10):1735-42. doi:10.1016/j.str.2013.08.005. Epub 2013 Sep 12.
The Hybridize mover samples structural combinations of multiple input models. It is used as part of the RosettaCM comparative modelling pipeline. For a more detailed description of its use for comparative modeling, see RosettaCM.
However, the mover may also be used more generally for structural modelling; several advanced options for that purpose are shown here.
The general input format is shown here:
<Hybridize name="&string" stage1_scorefxn="&sring" stage2_scorefxn="&string" fa_scorefxn="&string" batch="(1 &bool)"> <Template pdb="&string" cst_file="AUTO" weight="1.000" /> <Template pdb="&string" cst_file="AUTO" weight="1.000" /> ... </Hybridize>
Notice that the protocol proceeds by first selecting an initial template model, then sampling substructures from other templates. The weight variable only controls that first step. Thus, if you have very incomplete models, it is recommended to set them to weight 0: they will never be used as the starting models, but fragments from them will be recombined with other models.
Input fragment files may be given by adding the following tag withing the
<Hybridize ...>...</Hybridize> block:
<Hybridize ...> <Fragments three_mers="t000_.200.3mers.gz" nine_mers="t000_.200.9mers.gz"/> </Hybridize>
If not provided, fragments will be built automatically.
The following options control scoring:
The following options control the protocol flow:
The following options handle ligands:
More advanced options are highlighted in this section. Note that these may be experimental, so use at your own caution!
The following options may be useful for applying hybridize iteratively:
First, to start from an extended chain, use the following template tag:
<Hybridize ...> <Template pdb="extended" weight="1.0" cst_file="x.cst" /> </Hybridize>
If all other templates have zero weight, then the protocol will always start from a single extended chain (unless the add_non_init_chunks is also specified, in which case random rigid body transformations will be taken from other templates).
For fine control of protocol behavior, control the relative weights of individual moves:
The "AUTO" option for all of these scales the relative weights depending on input structure coverage/completeness. So adjust these with care!
Other fine-grained protocol control options:
The detailed controls block allows fixing certain substructures. It may be specified by adding the following tag withing the block:
<Hybridize ...> <DetailedControls start_res="273" stop_res="296" sample_template="0" sample_abinitio="0" task_operations="&string"/> </Hybridize>
This says that for residues 273-296, do not allow template hybridization moves (sample_template=0), and do not allow fragment insertion moves (sample_abinitio=0). If both are set to false for a region, that region will also not minimize in centroid (note that fullatom refinement ignores these flags, however).