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selection from a selection file

To perform a group 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 group selection file (see Fig. 4.30).

Figure 4.30: The group selection dialog for a selection from a selection file.

The format of a nMOLDYN group 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 deuteration to nested lists of integers where each nested list will generate a group of atoms whose PDB serial number match the integer of the nested list. An example of a deuteration selection file is shown in figure 4.31.

Figure 4.31: Example of a group file.

This example will create three groups. The first one made of atoms 1, 4, 9, 78, 101 and 134 of the PDB file, the second one made of the atoms 12, 23 and 192 and the third one made of the atoms 11, 26, 1023, 245 and 234.

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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