And to add another small item: the SOLOMON interface in SHARP allows
adjustment of the mean density depending on protein, DNA or RNA
content. See
http://www.globalphasing.com/sharp/manual/denmod2.html#MeanDensity
Cheers
Clemens
On Wed, Aug 19, 2009 at 09:26:34AM +0100, Gerard Bricogne wrote:
> Dear Ed,
>
> The question of dealing appropriately with density modification in the
> presence of "heavy atoms" has been discussed in the paper on SHARP 2.0 (see
> Acta D59, 2023-2030, published in 2003) and the solution described in that
> paper has been available in all versions of SHARP/autoSHARP since then.
> Essentially, it removes the contribution from the heavy atom(s) before
> density modification in SOLOMON, and adds it back afterwards. You might want
> to give it a try if you have had cases where you thought that density
> modification was doing a sub-optimal job with your metal-containing protein.
>
>
> With best wishes,
>
> Gerard.
>
> On Tue, Aug 18, 2009 at 04:42:48PM -0400, Edward A. Berry wrote:
> > Peter Grey wrote:
> >> Hi everyone,
> >> I am trying to use density modification at rather low resolution (4-5A )
> >> for an RNA structure. My first time ever with RNA.
> >> I usually use Histogram matching as part of the density modification
> >> scheme in DM. But this method is based on density distribution of protein
> >> maps I think.
> >> Is histogram matching still valid when it comes to RNA or protein/RNA
> >> structures ?
> >
> > I have the same question with respect to metalloproteins.
> > Presumably the heavier metal atoms make spikes that are completely off the
> > scale of a normal protein histogram. Is it then a bad idea to use
> > histogram matching? Do the metals get flattened down to the highest
> > density expected for protein on every cycle?
> >
> > Ed
>
> --
>
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> * Gerard Bricogne [log in to unmask] *
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