Thanks Jason.
That gives some idea about the origin of the problem. The structures are
different only in that they are taken from outputs of zdock and undergo
different rigid body transformations. Can that give rise to the difference?
Thanks .
On Tue, Jan 7, 2014 at 3:08 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Jan 6, 2014 at 12:42 PM, Sourav Purohit <sour000.gmail.com> wrote:
>
> > (The last mail had some error.)
> >
> > I applied bondbydistance command to a molecule many times independently
> > with default cut-off value. In the first trial leap recognised 279 (111
> non
> > H-H) potential bond pairs. In the second it recognised 277 (109 non H-H)
> > and in the third trial it was 278 (110 non H-H).
> > Shouldn't the number of potential bond pairs be the same in each trial.
> > What may the origin of the difference in the number of non-H-H potential
> > bond pairs.
> >
>
> Only if the input structures are _exactly_ the same. In many cases, even a
> simple rigid-body transformation in a PDB file (or another format with very
> low coordinate precision), the computed distances may change simply
> because the coordinates are held in such low precision that distances can't
> be computed more precisely.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Jan 06 2014 - 14:00:04 PST
