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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