Subject: Re: [modeller_usage] model.pick_atoms problem
From: Modeller Caretaker <>
Date: Thu, 06 Apr 2006 10:40:12 -0700
Cc:
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.