|
|
Predict Side Chains Panel |
Predict the conformation of side chains in one or more proteins by sampling orientations to minimize the energy. The sampling can include the orientation with respect to the backbone, and sampling of the backbone as well. The sampling can be run with periodic boundary conditions, in implicit solvent, and with an implicit membrane.
To open the Predict Side Chains panel, you can:
Choose Applications → BioLuminate → Loop + Sidechain Prediction → Predict Side Chains in the main window.
Choose Applications → Prime → Protein Refinement → Predict Side Chains in the main window.
Choose Tasks → Biologics → Loop + Sidechain Prediction → Predict Side Chains in the main window.
Choose Tasks → Protein Refinement → Predict Side Chains in the main window.
When selecting residues for side-chain prediction, you might want to use the Atom Selection dialog box, which provides proximity options that allow you to select all residues within a certain distance of a ligand, for example.
If you imported a PDB structure that has residues with missing atoms, you can select those residues by clicking Select Residues with Missing Atoms. The selection is based on the information generated when the structure was imported, and does not use the current structural information. The selection therefore includes any residues that were fixed since import.
If you are refining a homology model, you should consider refining residues whose side-chain coordinates did not come from the templates. These are residues for which the Homology Status is equal to 1 and 2. The backbone coordinates for residues with a Homology Status of 1 were taken from the templates, but not the side chain coordinates. For residues with a Homology Status of 2 (none of the coordinates came from the templates), you should consider doing a loop refinement first. You can select all residues with non-template side chains by clicking Select Non-Conserved Residues.
Choose the source of the structures for the current task.
If you chose File from the Use structures from option menu, enter the file name in this text box, or click Browse and navigate to the structure file. The name of the file you selected is displayed in the text box.
Choose a continuum solvation model for the refinement. The choices are:
Select the residues for side-chain refinement using the standard picking tools.
Select residues from an imported PDB structure that have missing atoms. The selection is based on the information generated when the structure was imported, and does not use the current structural information. The selection therefore includes any residues that were fixed since import. This button is displayed when you select Predict side chains from the Task menu.
Select residues from a homology model whose side chain coordinates were not derived from the templates. The atoms in these residues have a Homology Status property of 1 or 2.
Choose a sampling algorithm that allows for orientational changes and backbone movement. The Sampling algorithm option menu has these choices.
Default—Use the default algorithm, which varies only the side chains and keeps the alpha and beta carbons fixed.
Monte Carlo—Perform Monte-Carlo sampling of side-chain conformations. When this algorithm is selected, the Maximum number of structures to return option and text box becomes available.
With CA-CB vector sampling—In addition to the default algorithm, vary the orientation of the CA-CB bond by up to 30°.
With backbone sampling—In addition to the default algorithm, perform a loop prediction on three residues: the residue whose side chain is being predicted and the residue on either side.
Select this option to return more than one conformation of the side chains, and specify the number of conformations to return in the text box. Only available for Monte Carlo sampling.
Open the Predict Side Chains - Constraints dialog box, to set up distance (atom-pair) and Cartesian (initial position) constraints.
Open the Predict Side Chains - Options dialog box to set up options: use of an implicit membrane and crystal symmetry, the solvent dielectric constant, the random seed for side-chain prediction.
The Job toolbar is used to make settings for a job and to start it.
Enter a name for the job in this text box.
This button opens the Job Settings dialog box. The arrow to the right opens a menu, from which you can make settings or perform actions that are related to the job.
The menu items are described below.
This icon indicates when there are jobs running for the application that belong to the current project. It starts spinning when the first job starts, and stops when there are no more jobs running. If a job fails to start, it changes to an exclamation point.
Clicking the button shows a small job status window that lists the job name and status for all active jobs submitted from the current panel (for Jaguar and MacroModel this means all jobs from any of the application panels). You can double-click on a row to open the Monitor panel and monitor the job, or click the Monitor button to open the Monitor panel and close the job status window. The job status is updated while the window is open. If a job finishes while the window is open, the job remains displayed but with the new status. The rows are colored according to the status: yellow for submitted, green for launched, running, or finished, red for incorporated, died, or killed. Click anywhere outside the window to close it.
Run the job with the current job settings.
The status bar displays information about the current job settings for the panel. This includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. It also displays a message for a short time when you start a new job.
The status bar also contains the Help button, which opens the help topic for the panel.
|