Input Data Dialog Box

Input Data Dialog Box Features

• Use structure from options
  • File name text box and Browse button
  • Assign bond orders option
• Use sequence from options
• Reflection data input controls
• Space group section
• Unit cell parameters section
• Calculation Settings button

Use structure from options

These options allow you to specify the source of the initial guess at the structure. The two options are:

• File — Read the initial guess from a file, using the File name text box and Browse button. The space group and cell parameters are also read from the file if possible, and replace existing definitions.

• Workspace — Use the structure in the Workspace as the initial guess.

File name text box and Browse button

Enter the file name in this text box, or click Browse and navigate to the file. The name of the file you selected is displayed in the text box. The allowed file types are: Maestro, PDB.

Assign bond orders option

Prepare the structure by assigning bond orders when the structure is imported. Metal atom requirements are handled automatically on input. If you do not use this option, you can perform these tasks beforehand (or later) using the Protein Preparation Workflow Panel.

Use sequence from options

These options allow you to specify the source of the protein sequence. This sequence is also known as the reference sequence. The two options are:

• File — Read the sequence from a file, using the File name text box and Browse button. The file must be in PDB, Maestro, or FASTA format, and there must be a 1:1 correspondence between the chains in the file and the chains in the input structure.

• Workspace — Use the sequence of the structure in the Workspace as the initial guess.

Reflection data input controls

Specify the file containing the reflection data. You can specify the file name in the text box, or click Browse and navigate to the desired file. In addition to the reflections, the space group and cell parameters are read from the file if they are available and can be read by Maestro, and replace any existing definitions. PrimeX can also make use of phased reflections to display maps and for use in real-space calculations.

If the reflections are read from an .mtz file, the properties for Fobs, Sigma, and the test set must be assigned from the properties in the file. When you click OK in the file selector, a dialog box opens that allows you to select a property for Fobs, Sigma, and the test set. For the test set, you can choose None to ensure that a test set is not read from the reflection file. By default, the test set from the reflection file is used.

If the reflection data file contains a test set, this set is used. If the reflection data file does not contain a test set, or the test set is inadequate, the Input Data – Test Set dialog box opens. This dialog box displays the number of reflections, and allows you to select a random test set, by percentage or by number of reflections. Note that this selection is made before rejecting any reflections, so it is possible that reflections in the test set could be discarded.

 

Space group section

In this section you specify the space group. You can enter the group number in the text box, or click Choose and choose the space group from the list provided in the Choose Space Group dialog box. If the structure file contained information on the space group, this information is automatically displayed, but can be changed to the relevant space group.

Unit cell parameters section

In this section you can specify the unit cell parameters. The parameters are automatically read from the reflection data file, and you can adjust them if you wish.

Note: You can only adjust these parameters in this dialog box. Although in principle you could edit the values in the Project Table, this does not change the parameters used by PrimeX.

Calculation Settings button

This button opens the Calculation Settings Dialog Box, in which you can set the resolution limit, overall B-factor scaling, choose a bulk solvent correction, set limits for rejecting reflections, choose whether to include hydrogen atoms in the output, specify restraints on planar groups, and set various real-space refinement options.