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Refine Loops - Options Dialog Box |
In the Refine Loops - Options dialog box you can select options for the loop refinement, including use of an implicit membrane and crystal symmetry, choosing the method, options, and job management.
To open the Refine Loops - Options dialog box, you can:
Click Options in the Refine Loops 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 the side-chain
prediction part of loop building.
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.
Select the method for refinement of multiple loops.
Select this option to refine two loops together. Each loop is refined in turn until the refinement has converged for both loops. You must have only two loops selected to use this option.
Select this option to refine each loop independently. The option menu provides three levels of sampling accuracy: Default, Extended, Ultra Extended. The menu items also include an estimate of the number of subjobs that will be run, so you can choose an appropriate number of processors. The text below the option and menu displays the recommended loop length for the selected accuracy. If you select Ultra Extended, you can only refine one loop at a time.
These options allow you to set a limit on the the number of processors
over which to distribute the loop sampling subjobs. Each sampling method runs in
several stages, and each stage can use a different number of processors.
Some methods have a fixed maximum number of processors that they can use.
For these methods, increasing the number of processors beyond this number
does not affect the time taken for the job.
To make use of as many processors as are available, select
Distribute over maximum available processors.
To set the maximum number of processors, select
Distribute over and enter a value in
the text box.
Filter the output from the loop prediction.
To return more than one structure, select Maximum number of structures to return and enter the number of structures in the text box. The default when this option is selected is 4.
To filter the structures by energy, select Energy cutoff and enter an energy value in kcal/mol in the text box. Structures whose energy is higher than that of the lowest-energy structure by more than this amount are not returned. The default cutoff when this option is selected is 10 kcal/mol.
To limit the extent to which alpha carbon atoms can move from their original positions, select this option, and enter a limit in the text box. The default distance is 3.00 Å. The extended sampling procedure tests multiple values for Maximum CA movement, and therefore this option is unavailable when any of the extended sampling options has been selected.
Select this option to allow side chains within the specified distance of the chosen loop to be adjusted during the refinement, and specify the distance in the text box. Side chains are included in the refinement if the distance between any heavy atom in the side chain and any CB atom in the initial set of loop structures is less than the specified distance. The default distance is 7.50 Å.
Specify the minimum allowed distance between atoms as a fraction of their van der Waals radii. The default value is 0.70, meaning that the distance between atoms must be at least 70% of their ideal van der Waals separation. The extended sampling procedure tests multiple values for the minimum overlap and therefore this option is unavailable when any of the extended sampling options has been selected.
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