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 > > -- > > =============================================================== > * * > * Gerard Bricogne g...@globalphasing.com * > * * > * Global Phasing Ltd. * > * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * > * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * > * * > =============================================================== -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************
