1 Frame range

The user can specify the minimal (x) and maximal (y) serial numbers of frames with the use of switch –n x-y at MobyWat command line. Please, be sure that the frames exist in your trajectory input files.

2 Molecular ranges

MobyWat requires definition of target and waters in the frames using –t and –w switches of the command line, respectively. There are three possibilities of definition.

1) Ranges of atom serial numbers can be given using minimal (x) and maximal (y) serial number in a form of –t x-y or –w x-y.

2) In the case of target, a list of one-letter chain IDs such as xy… can be also used in a form of –t [xy…]. Note, that use of […] brackets is obligatory. This option is especially useful if atom list of target is non-continuous in the frame, and the target is stored in several chains.

3) In the case of waters, definition is also possible by specification of a single residue name such as WAT in the form –w WAT. MobyWat can automatically detect and assign water molecules in the frame using the –w Auto command line entry, as well. During automatic detection residue names SOL, WAT and H2O can be identified.

Besides their use for frames in the command line, the above specifications of molecular ranges can be used for the reference structure in Analysis mode and Validation sub-mode.