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selection from a selection file

To perform a subset selection from a selection file, you have to click on the from a selection file radiobutton. A dialog will be displayed in the underneath frame from which you will be asked for a subset selection file (see Fig. 4.20).

Figure 4.20: The subset selection dialog for a selection from a selection file.

The format of a nMOLDYN selection file is quite simple. It is an ASCII file with the .nms extension whose contents is a python script made of two lines. The first line must set the variable pdb to the path of a PDB file of the first frame of the trajectory being processed (it can be obtained using the frame extractor tool described in section 4.1.3 for example).The second line must set the variable subset to a list of integers where each integers represents the PDB serial number of the atoms to select. An example of a subset selection file is shown in figure 4.21.

Figure 4.21: Example of a subset file.

Once a selection file has been loaded, the constructed selection string that will be used by nMOLDYN for this kind of selection is displayed in the Selection preview entry at the bottom of the dialog with highlighted keywords.

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