Refine Loops - Options Dialog Box

Refine Loops - Options Dialog Box Features

• Environment options
• Seed options
• Dielectric text box
• Method options
• Subjobs options
• Output for single loop feature options
• Maximum CA movement option
• Refine side chains within option
• Minimum distance text box

 

Environment options

These options allow you to specify the environment of the protein, other than the use of an implicit solvent.

Default option

Use the environment specified in the main panel, which could be a vacuum or an implicit solvent.

Implicit membrane option and Set Up Membrane button

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. Hydrophilic groups lose any short-ranged solvation energy from the high dielectric region when placed in 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.

Crystallographic unit cell option

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.

Seed options

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.

Dielectric text box

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.

Method options

Select the method for refinement of multiple loops.

Cooperative loop sampling option

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.

Serial loop sampling option and menu

Select this option to refine each loop independently. The option menu provides three levels of sampling accuracy: Default (up to 5 residues), Extended (6 to 11 residues), Ultra Extended (10 or more residues). 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.

Extended sampling samples loop conformations more thoroughly, using a series of loop constraint settings. Up to eight processors can be used simultaneously to perform loop refinement. If you select Ultra Extended, you can only refine one loop at a time.

Subjobs options

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. The maximum number of processors that can be used by the different sampling methods are:

Default	1
Extended	4
Ultra Extended	8*L (L is the loop length)

Output for single loop feature options

These options determine how many structures are returned:

• Maximum number of structures to return: Select this option to return more than one structure for each loop specified for refinement. The default when this option is selected is to return 1 structure for each loop.

• Energy cutoff: Select this option to prevent higher-energy structures from being returned, 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 the specified amount are not returned. The default cutoff is 10 kcal/mol.

Maximum CA movement option

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 3.0 Å. The extended sampling procedure tests multiple values for Maximum CA movement, so this option is unavailable when any of the extended sampling options has been selected.

This option applies to all alpha carbon atoms. For more control over which alpha carbons are restrained and by how much, use spatial constraints, which are described in Applying Constraints for Protein Refinement.

Refine side chains within option

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.

Minimum distance X of vdW radii text box

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.