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Refine Protein-Ligand Complex - Options Dialog Box |
In the Refine Protein-Ligand Complex - Options dialog box you can select options for refinement of a complex, including use of an implicit membrane and crystal symmetry, the solvent dielectric constant, algorithm selection, and options for each algorithm.
To open the Refine Protein-Ligand Complex - Options dialog box, you can:
Click Options in the Refine Protein-Ligand Complex panel.
The features in this dialog box depend on the sampling algorithm chosen in the Refine Protein-Ligand Complex panel.
These options allow you to specify the environment of the protein, other than the use of an implicit solvent.
Use the environment specified in the main panel, which could be a vacuum or an implicit solvent.
This option embeds the protein in an implicit membrane. The membrane is a low-dielectric slab that simulates the hydrophobic interior of a membrane. The membrane region is treated in the same way as the high-dielectric implicit solvent region. Hydrophobic groups, which normally pay a solvation penalty for creating their hydrophobic pocket in the high dielectric region, do not have to pay that penalty while in the membrane slab. Conversely, hydrophilic groups lose any short-ranged solvation energy from the high dielectric region when moving into the low dielectric region.
The option itself does not add a membrane. To run a refinement with a membrane, you must either add it in the Prime Membrane Setup panel, or select a project entry for refinement that already has a membrane. To set up the membrane, click Set Up Membrane button. In the Prime Membrane Setup panel you can set the membrane parameters, and place and adjust the membrane. The membrane parameters are stored with the project entry, so you do not need to set up the membrane if the entry already has one.
If crystal symmetry is known for this protein, apply periodic boundary conditions so that the crystal symmetry is satisfied. The protein is refined in the presence of its crystallographic neigbors.
Specify the seed for the random-number generator used in various sampling
methods.
Random: use a random seed.
Constant: use the integer given in the text
box as the seed.
Set the dielectric constant for the (continuum) solvent. Note that the solvation models also use a radius parameter, so changing the dielectric constant on its own is not the same as changing the solvent model, unless the radius of the desired solvent is similar to that of the solvent model. The default value is for water.
Set the number of passes through the prediction of side chains and minimization of the protein residues. Each pass consists of a side-chain prediction, followed by a minimization of the protein residues. The ligand is minimized with the rest of the protein after the specified number of passes is complete.
Set the maximum number of structures to return from the sampling. The number of structures is limited by the number of clusters formed when sampling the ligand dihedrals, so it may be less than the maximum set in this section.
Set parameters for the Monte Carlo sampling of the refinement region.
Specify the number of steps to take in the minimization. These steps are the "outer" steps, in which the long-range forces and the interaction with the solvent are updated. The number of "inner" steps (moves), in which short-range forces are updated, is set to an optimal value. The random selection of the type of move is made for each outer step, so the inner steps are all moves of the same type.
Specify the probabilities of making each of three kinds of moves. These probabilities can be used to guide the minimization. The numbers you enter are relative frequencies of each move, so they do not have to sum to 1.
Choose an option for the kind of structure to return.
Set options for hierarchical optimization.
Specify the number of clusters to use when clustering the conformations of the complex. A k-means algorithm is used for the clustering.
By default, only one structure is returned. If you want to examine multiple possible structures, specify the maximum number to return in this text box. The number of structures is limited also by the number of clusters.
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