Thanks for the reply, Ben. I have implemented the patch successfully.
Saludos, Ignacio
On Tue, May 21, 2013 at 7:19 PM, Modeller Caretaker < modeller-care@salilab.org> wrote:
> 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 > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >