Re: [modeller_usage] how to build a model from a template with only CA atoms?
To: Lixia Jin Day <>
Subject: Re: [modeller_usage] how to build a model from a template with only CA atoms?
From: Modeller Caretaker <>
Date: Tue, 25 Nov 2008 11:04:03 -0800
Lixia Jin Day wrote:
> I have a protein conformation with only alpha carbon (CA) atoms. And I
> want to build up the full structure without moving the position of the
> CA atoms. Can I do it with MODELLER? How to do it?
Did you look at http://salilab.org/modeller/FAQ.html#12 ?
If you don't want to change the protein sequence (i.e. you're not really
doing "homology modeling") then you can just feed a Modeller a 1:1
alignment between two copies of the same sequence and use automodel. If
you really don't want the CA atoms to move at all, see
You can use a selection such as
s = selection(self)
return s - s.only_atom_types('CA')
You could also use complete_pdb() to fill in the non-CA atoms rather
than using automodel. But this creates the coordinates from internal
coordinates only, so may lead to steric clashes.
Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage