Alex Brown wrote: > This may, or may not, be a problem, but I have found that using the > selection_segment argument ‘FIRST:A’ , ‘LAST:A’ in model.pick_atoms > doesn’t appear to work properly. In fact, the whole molecule (all > chains) is selected (i.e. the argument acts as if it were ‘FIRST:’, > ‘LAST:’). Correct selection does occur if discrete, numbered residues > are used, as in ‘1:A’, ‘100:A’, selecting atoms in a segment from > residues 1 to 100 in chain A.
The documentation is perhaps a little misleading; you can't use FIRST or LAST for selection_segment (it's only valid in an alignment file, or for model_segment when reading a PDB file). If the residue:chain is not found (as will be the case if you use FIRST or LAST) Modeller defaults to an all-atom selection.
The pick_atoms command will be replaced with a more flexible selection method in the next Modeller release.
Ben Webb, Modeller Caretaker