I think 400 protein models in a single multi-model PDB file is problematic.
30,000 x 400 = 12,000,000 atoms.
On Fri, Jan 30, 2015 at 10:14 AM, Rolf Huehne <rhue...@fli-leibniz.de>
wrote:
> On 01/30/2015 04:30 PM, Robert Hanson wrote:
> > alt-loc should be fine; the entire group is being replaced, so there is
> no
> > problem with names. Can't help with the 400 -- even if you could do that,
> > you would not want to using Jmol, I think. Better tools for that. But for
> > small numbers, we could add mutations as alt-loc. Actually, that's a lot
> > easier that creating a whole new group. Way before 400 you will run into
> > the problem that the allowed number of bonds that link residues will be
> > exceeded (20? something like that).
> >
> One advantage of adding the mutated residues is that there are no such
> limits.
>
> Bob, why do you think that Jmol wouldn't be suitable for doing 400
> independent single residue mutations?
>
> If it is suitable for doing each of them individually, why shouldn't it
> be suitable for all of them consecutively (all done on the original
> structure)?
> Maybe performance could be a problem but we will have to see how
> performance will be after sidechain positioning optimizations have been
> added. And the two specialized programs we are using to precompute the
> mutations can also take several minutes for one PDB entry.
>
> Regards,
> Rolf
>
>
> --
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> Rolf Huehne
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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