Calculation Settings Dialog Box

Calculation Settings Dialog Box Features

• Resolution limits options
• Bulk solvent correction controls
• Overall B-factor scaling options
• Reject reflections with option and text boxes
• Use implicit solvent option
• Include H atoms in structure output option
• Planar group restraints options
• Maximum memory use in FFT text box
• Real-space options section
• Set Default Map Colors button

 

Resolution limits options

There are two options for setting resolution limits for the reflection data:

Calculate from data and cell constants option

Calculate the values inherent to the data. This option is useful if you have set resolution limits with the Use values option and want to return to the values defined by the data.

Use values option

Use the values supplied in the Low and High text boxes as the resolution limits. Only the reflection data that lie between these two limits are used in the calculation. The limits can be changed for different stages of the refinement process. The initial values are set from the reflection data on input.

The limits can be changed for different stages of the refinement process. You might, for example, want to set the high-resolution limit to 4 Å for the rigid-body refinement, then change it back for the following stages.

Bulk solvent correction controls

There are three options for bulk solvent correction: None, Babinet, and Mask. The Babinet method is less accurate, but does not depend on having a good estimate of the structure. The Mask method relies on a definition of the boundary between the protein and the solvent, and is controlled by the following three parameters:

• VdW radius for covalent atoms — Van der Waals radius of covalently bound atoms. This radius is larger than normal van der Waals radii, to eliminate small regions that should not be considered as bulk solvent regions.

• Shrink factor — This factor is applied to reduce the covalent radii once the solvent regions are identified.

• Radius for ions — Van der Waals radius for atoms in ions. These are explicitly identified ions, which are usually in the first solvation shell.

The default values of these parameters are usually satisfactory.

Overall B-factor scaling options

There are three options for overall B-factor scaling:

• Anisotropic—A single anisotropic scaling factor is optimized. Both isotropic and anisotropic components of this scale factor are applied, to the isotropic B-factors and to Fo, respectively. This option is useful in most circumstances, and is also the default.

• Isotropic—Overall scaling is applied only to isotropic B factors.

• None—No scaling is performed.

Reject reflections with options and text boxes

This option enables the rejection of reflections based on cutoffs on their F values, which allows you to filter reflection data that are either too weak or too strong. When you change any cutoff, the number of reflections rejected is displayed to the right of the text box.

• F/sigma(F) < cutoff —Reject reflections for which the ratio of the F value to the standard deviation of the F values is less than the cutoff. This criterion eliminates reflections with large relative errors.

• F < cutoff—Reject reflections for which the F value is less than the cutoff. This criterion eliminates reflections with small amplitudes.

• F/rms(F) > cutoff—Reject reflections for which the ratio of the F value to the root-mean-square F value is greater than the cutoff. This option eliminates reflections with high relative amplitude, which might dominate the Fourier series and introduce large amounts of noise if they are in error.

Use implicit solvent option

This option allows you to use a surface generalized Born (SGB) implicit solvation model for the solvent regions when performing real-space refinements of any kind or reciprocal-space minimizations and rigid-body refinements.

Include H-atoms in structure output option

This option allows you to include the positions of hydrogen atoms in the output structure.

Proper handling of hydrogens is critical in PrimeX. The presence of hydrogens is essential in any of the calculations that use force fields, because PrimeX uses the OPLS all-atom force fields. Once you have added hydrogens, and optimized their positions, you should retain them for the rest of the calculation. Although the hydrogens can be added back after they have been removed, their placement will not be optimal. The Include H-atoms in structure output option allows you to include the positions of hydrogen atoms in the output structure.

When PrimeX adds hydrogens, it does so in an intelligent manner during preprocessing, with consideration of possible hydrogen bonding partners. However, hydrogens already present in the structure are not optimized during this procedure, on the assumption that their positions have already been optimized to some degree. Hydrogen bonding networks are additionally optimized using a Monte Carlo procedure in the task Optimize H-bond Networks. In this task, additional orientations of asparagine, glutamine, and histidine side chains, the charge state of ionic groups, and the tautomeric state of histidines, are all considered while optimizing hydrogen-bond formation.

Planar group restraints options

These options allow you to choose how to restrain groups that are supposed to be planar, such as peptide linkages. The restraints are applied to the improper torsions. There are three options:

• Low—Allow the improper torsions to be determined solely by the force field, without further restraint.

• Normal—Apply a moderate restraint to improper torsions over what is already in the force field, typical of that used in other refinement programs.

• High—Apply a high level of restraint to improper torsions over what is already in the force field.

Small deviations from planarity are not unphysical, as the potential well that preserves planarity has a finite depth and width. However, deviations can be an indication of the need for more refinement.

Maximum memory use in FFT text box

This text box allows you to set a limit on the memory used by the fast Fourier transform code, in MB. Larger values will result in faster calculations, but this value should not exceed the available physical memory. The default value is a safe choice for all but the most limited of computer hardware.

Real-space section

In this section, you can select options to specify the source of the phases used to generate the map, set the weighting factor for the balance between force field and electron density terms, and set the initial B-factors of the atoms.

Observed amplitudes and phases calculated from model option

With this option, phases are calculated from the model using the observed amplitudes. This is the default option.

Amplitudes and phases from file option and controls

With this option, phases are obtained from a file that contains phased reflections. When you select this option, the Browse button becomes available, and you can enter the file name in the text box or click Browse and navigate to the file in a file chooser.

Weighting factor text box

Set the relative weighting factor for the X-ray (electron density) terms in the function that is minimized in the refinement. PrimeX computes a fairly optimal weighting of the force field and X-ray terms by default.

Set B-factors of atoms to be fit to option and text box

Set the B-factors of the atoms that are to be refined to the value in the text box. Using a relatively small value ensures that the real-space refinement is not trying to fit to an electron density that is too spread out.

Set Default Map Colors button

This button opens the Set Default Map Colors Dialog Box, in which you can set the default colors for each type of map.