On 05/15/2013 03:47 PM, Ignacio Ibarra wrote:

I would like to remove the initial phosphate group declared in the first
residue of each nucleic acid chain. Those atoms should not be present in
real structures. I would like to do it without writing new text in the
.lib files that are into the modlib folder

What you're describing is a patch. Patching is done automatically for you for amino acids chains, but no automatic patching is done for nucleic acids - you need to do this manually. You probably want the 5TER and 3TER patches (look for the PRES 5TER line in modlib/top_heav.lib) but there are other kinds of modifications in there too, such as 5MET (which also removes O5'). Patches are usually applied in the special_patches() method, e.g.

class MyModel(automodel):
    def special_patches(self, aln):
        # Patch the nucleic acid chain that runs from residue 10 to 20:
        self.patch(residue_type='5TER', residues=self.residues['10'])
        self.patch(residue_type='3TER', residues=self.residues['20'])

a = MyModel(env, alnfile=...

See also
http://salilab.org/modeller/9.11/manual/node24.html

I read about a pick_atoms() method in an older version of MODELLER, but
it is not commented in the 9v11 manual
(http://binf.gmu.edu/software/MODELLER/node131.html)

The official URL here should be
http://salilab.org/modeller/8v0/manual/node131.html

Is there something
similar currently available for removing atoms from the model in the
automodel or another class?

Sure, pick_atoms() was replaced by the much more versatile selection class:
http://salilab.org/modeller/9.11/manual/node225.html

        Ben Webb, Modeller Caretaker
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