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selection from a selection file

To perform a deuteration 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 deuteration selection file (see Fig. 4.25).

Figure 4.25: The deuteration selection dialog for a selection from a selection file.

The format of a nMOLDYN deuteration 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 a list of integers where each integers represents the PDB serial number of the atoms to select. An example of a deuteration selection file is shown in figure 4.26.

Figure 4.26: Example of a deuteration 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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