Manual

This module has been devised to allow the unattended processing of several files, from the bead model generation to the computation of the hydrodynamic parameters. The operations begin by loading the files in the module via the Add Files button. Several files can be loaded at the same time from the same directory location. Files can be of both kinds supported by US-SOMO, PDB structures or bead models. If unwanted files have been inadvertently loaded, or they are found later to be not suitable for processing (see below), they can be removed from the list by clicking on them and pressing the Remove Selected button. Once the list is completed, a single file can be selected by clicking on it, and multiple files can be selected by clicking on them while holding the shift key. Select All will obviously select all files.

In order to allow for the unattended operations, the files must be checked for compliance with the US-SOMO requirements. In particular, their residues must be defined in the somo.residue lookup table and must contain all atoms. Alternatively, the parsing options can be set so to cope with these eventualities, by either skipping the incomple/not coded residues, or by the use of approximate methods (a detailed description of these options can be found here). For bead models, they must match the overlap tolerance as set in the Hydrodynamic Computations Options module.
The uploaded files are therefore screened for compliance with the settings shown in the Screen selected files: panel, by pressing the Screen Selected button. The progress window on the right side reports the progress of the operations, and list the problems that might be found with the files, prompting for corrective action to be taken.

The sequence of batch operation is then set in the Process selected files: panel:

The alternative Process Only First Model in PDBs with Multiple Models and the Process All Models in PDBs with Multiple Models clickboxes control if just the first or all models should be processed in PDB files containing multiple models, like those derived from NMR studies. These options are active only if at least a PDB file is among the selected files.

The alternative Build SoMo Bead Model and Build AtoB (Grid) Bead Model dictate which bead modeling procedure will be used to generate the models. These options are active only if at least a PDB file is among the selected files.

The Calculate Hydrodynamics checkbox enables the computation of the hydrodynamic parameters after the bead model building phase is completed.

Selecting the Single Hydro Results File: checkbox will produce a single results' file, with at the end the averages of all parameters, instead of separate files for each model uploaded or generated. A filename for the single results' file must be provided in the dedicated space. Otherwise, each file will be named using the general US-SOMO rules and the prefixes present in the main program panel.

A subset of parameters can be saved in another file in a comma-separated format by selecting the Save parameters to file clickbox. The parameters to be saved can be selected from the dedicated module (see here) accessed by pressing the Select Parameters to be Saved button.

When all the preliminary operations have been completed, the batch operation can be launched by pressing the Start button, and the progress will be reported in the progress bar and in the right-side progress window. Operations can be aborted at any time by pressing the Stop button.

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Last modified on February 1, 2010.