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