On Mon, 5 Mar 2007, Fred. Vellieux wrote:
> Hi James,
>
> I tried to increase the parameter value to 3.0 A. The resulting file gives
> the same behaviour (and the newly introduced OXTs are within 0.05 A of the
> N atom of the following residue) so I think the distances are reasonable.
>
> So unfortunately I think your valuable suggestion does not solve the
> problem. On the graphics with Coot the starting model looks fine in these
> regions.
>
> I need to keep the automatic mainchain break detection because there are
> some gaps in each chain of the model (12 chains in all).
>
> So if there are other suggestions to solve this b....r of a problem, they
> are most welcome!
>
> Fred.
Hello again,
I believe that I found the cause of the problem and a solution to it:
not by looking at the molecule with Coot but by looking at the separate
PDB input files where the problems occur.
They all share the same features: the chain label used by CNS is kept
along within Coot. For the parts that are modelled de novo using Coot, the
output pdb file does not contain the CNS chain label. It is only at those
positions where there is a discontinuity for chain label present or absent
does CNS introduce an extra OXT atom. I have introduced the missing chain
labels where necessary, and I am testing this right now:
the file produced by the generate script now does not contain added OXT
atoms.
I thought I'd inform the bulletin boards of this annoying feature.
Fred.
--
Fred. Vellieux, esq.
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