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Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design Jared Adolf-Bryfogle, J. W Labonte, J. C Kraft, M. Shapavolov, S. Raemisch, T. Lutteke, F. Dimaio, C. D Bahl, J. Pallesen, N. P King, J. J Gray, D. W Kulp, W. R Schief bioRxiv 2021.09.27.462000; https://doi.org/10.1101/2021.09.27.462000
Autogenerated Tag Syntax Documentation:
A metric to measure hydrogen bonds between a set of residues that are water-mediated.
DEPTH: Depth is set to a default of 1 (IE a single water mediates the hydrogen bond). Make sure to set the -ignore_waters flag to false in order to have Rosetta include the HOH residues.
SELECTION: If one residue selector is given, will calculate bridged water paths between residues of the selection and all [OTHER] residues that are not water, otherwise it will calculate bridges between one selection and another.
If NO SELECTION is give, will report ALL bridged hbonds in a pose [by default without self-water-self hbonds]. HBONDS: Since these are bridged hbonds, and h-bond networks can be rather complex, the numbers reported here are the unique h-bond paths from sele1 to sele2. If you give only a single residue selector, these are bridged hbonds from sele1 to OTHER residues in the pose not including water. Pass the same selection to get internal bridges of a selection. By default we do not include mediated hbonds back on itself, but this is an option.
TIPS: It is generally recommended to repack the waters using the OptH TaskOperation before input into this metric, especially if only Oxygens were present.
Using the option -include_vrt false will keep all waters present in the resulting structure. Use the option -corrections::water::wat_rot_sampling 10 to decrease the angle of sampling from a default of 30 to 10 or 15. This will result in many more rotamers (and run-time), but will improve networks.
Hydration shells can be calculated by passing selection1 as all waters in the pose, selection2 as the protein or chain, and then reporting only a single depth (with max_depth at 0 and 1) for the first and second shell waters. Post-processing will be needed. Finally, it is generally recommended to use the -beta_nov16 and -genpot scorefunctions as this can result in better h-bond detection. Both of these have been published and can be turned on together using the -beta flag.
AUTHORS: Jared Adolf-Bryfogle (email@example.com) Citation: De-Novo Glycan Modeling in Rosetta (drafting)
Ryan Pavlovicz (Rosetta-ECO: Explicit Consideration of cOordinated water) Citation: 'Efficient consideration of coordinated water molecules improves computational protein- protein and protein-ligand docking', biorxiv, PLOS CB in-review
<WaterMediatedHbondMetric name="(&string;)" custom_type="(&string;)" output_as_pdb_nums="(false &bool;)" residue_selector="(&string;)" residue_selector2="(&string;)" depth="(1 &positive_integer;)" include_only_set_depth="(false &bool;)" include_self="(false &bool;)" include_virt_waters="(false &bool;)" />
ExplicitWaterMover: Add and sample Explicit waters in Rosetta
ResidueSummaryMetric: Summarize a PerResidueRealMetric in various ways, such as the mean, sum, or the number of residues above, below, or equal to a certain value.
RunSimpleMetrics: Run a set of SimpleMetrics and output data to the scorefile