covalent bond between symmetry related halves of a spermine molecule (fwd)

s_aarono at EDUSERV.ITS.UNIMELB.EDU.AU s_aarono at EDUSERV.ITS.UNIMELB.EDU.AU
Wed Feb 21 21:08:58 EST 1996


On Thu, 22 Feb 1996, Gerard 'CD' Kleywegt wrote:

> >In this regime, the enery between your ligand and itself won't
> >be calculated, so there will be no self repulsion.
> 
> nor will the ligand obey the crystallographic symmetry
> (unless you introduce strong "ncs" restraints internally)

Yes. I forgot to mention this.

> 
> a much simpler solution is to use a strong harmonic
> restraint on the offending carbon (you have to put
> it into the density such that it is at a normal
> distance from its symmetry mate; use the symm_sphere
> and dist_def or neigh_at commands in O)
> alternative: fix the carbon entirely (but it think
> a harmonic restraint is better)

But what about stereochemistry? X-plor needs to know about
the bonds, angle (and impropers and dihedrals, if any) across
the interface. If you just have half a molecule restrained
at a point, how will x-plor take this into account?


Aaron





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