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Input Data Dialog Box |
In this dialog box you specify the source of the model structure, sequence, reflections, and optional map, and set the space group and unit cell parameters. When you click OK, the data is copied into the project and any requested initial processing is performed.
To open the Input Data dialog box, you can:
Click Input Data in the PrimeX panel.
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. You can specify the file name in the File name text box, or click Browse and navigate to the desired file. The file must be in PDB or Maestro format. 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.
In addition, the Assign bond orders option prepares the structure by assigning bond orders and treating metal atoms when the structure is imported. If you do not use this option, you can perform these tasks later using the Protein Preparation Wizard panel.
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. You can specify the file name in the File name text box, or click Browse and navigate to the desired file. The file must be in PDB, Maestro, or FASTA format.
Workspace — Use the sequence of the structure in the Workspace as the initial guess.
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.
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.
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.
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.
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.
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