Re: [modeller_usage] Transfer_xyz or other methods?

[Modeller Caretaker <>]

 wrote:
> I appreciate for taking time and explaining in detail. Its not that I
> don't want to use automodel. But I have two questions
> 
> 1. Is modeller going to accept the .ini file (I converted it to .pdb
> manually) with undefined coordinates (999 numbers) in a script described at
> 
> http://salilab.org/modeller/manual/node26.html
> # Modeling using a provided initial structure file (inifile)

Sure - Modeller will accept any model provided it has the same sequence
as your target sequence.

> 2. If I use automodel, I will again end up with an automated model where
> I loose the bacbone Calpha conformation. i.e. my goal to retain backbone
> conformation (for which I used transfer_xyz) will not be achieved.

You can keep some of the atoms fixed during the refinement; see
http://salilab.org/modeller/9v5/manual/node23.html

In your case I guess you'd want to select everything but mainchain (or
just C alphas) in aligned regions. You could do that with something like
the following as your select_atoms() method:

    def select_atoms(self):
        aligned_regions = selection(self.residue_range('1:', '10:'),
                                    self.residue_range('20:', '30:'))
        aligned_backbone = aligned_regions.only_mainchain()
        # or
        # aligned_backbone = aligned_regions.only_atom_types('CA')
        return selection(self) - aligned_backbone

Alternatively, you could have Modeller determine your insertions
automatically with model.get_insertions() - see
http://salilab.org/modeller/9v5/manual/node162.html

Since this returns a list of all residue ranges that are aligned with
gaps in your template, it is essentially the inverse of aligned_regions
above, so you could say something like

aln = self.read_alignment()
aligned_regions = selection(self) - \
                  selection(self.get_insertions(aln, 0, 100, 0))

	Ben Webb, Modeller Caretaker
-- 
             http://www.salilab.org/modeller/
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