Re: [modeller_usage] Bad Contacts and Dimeric symmetry

[Modeller Caretaker <>]

nornik wrote:
> My first issue is about bad contacts. When i produce models and
> evaluate them with procheck I always get some bad contacts. I have
> checked the procheck  output files and noticed that all bad contacts
> always have a distance of 2.5 or 2.6 angstroms. Is there any way to
> change the minimum distance between atoms (i.e. increasing the
> different atom radii), since it seems like modeller and procheck have
> different opinions about what a bad contact is?

Bad contacts are usually a consequence of a poor input alignment, 
causing conflicts between different classes of restraints. You can 
certainly modify the atomic radii (modlib/radii.lib file) but this will 
probably not fix your underlying problem.

> My second issue is about dimeric symmetry. I produced a model of a
> dimer using the automodel class and got some nice models. Then i wanted
> to produce the dimers with symmetry restraints and got many angles in
> disallowed regions, many bad contacts and very low G-factors. This seems
> very strange since the only difference between my two runs was that i
> requested symmetry in my second run. Why do my symmetrical dimers become
> so bad?

Was the first (unconstrained) dimer model roughly symmetric? If it 
wasn't, then trying to force it to be symmetric by imposing a symmetry 
restraint probably won't help - there are probably some conflicting 
restraints (particularly if your template is a non-symmetric dimer, 
since the distance restraints from the template will conflict with your 
symmetry). You may need to remove some of these restraints, either 
manually or by modifying your alignment.

...
>         s1 = selection(self.chains['A'])
>         s2 = selection(self.chains['B'])

I doubt this is the cause of your problem, but symmetry restraints will 
only work if these two chains are in fact the same sequence, since they 
work by constraining all internal distances between the two selections.

You can also speed things up a lot by only constraining the backbone or 
C-alpha atoms to be symmetric, since that will dramatically cut down on 
the number of internal distances, e.g. with

        s1 = selection(self.chains['A']).only_atom_types('CA')
        s2 = selection(self.chains['B']).only_atom_types('CA')

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