Re: [ccp4bb] Histogram matching in DM - question
Hi Peter, You can specify in DM the mean density of the protein region in the SOLC keyword. However I am not sure this will affect the density distribution used for histogram matching. All the best, Adam.
Re: [ccp4bb] Histogram matching in DM - question
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) ***
Re: [ccp4bb] Histogram matching in DM - question
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 * * * ===
Re: [ccp4bb] Histogram matching in DM - question
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
Re: [ccp4bb] Histogram matching in DM - question
Hi Peter, Histogram matching works well for RNA structure, but be aware that density modification in general can be very tricky at low resolution. If by any means you can exploit averaging, e.g. multicrystal averaging of non-isomorphous crystals, it will probably be very helpful. It will also depend on the source of your phases Poul On 18/08/2009, at 21.43, 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 ? And a general question regarding density modification and RNA structure. Can statistical density modification programs (RESOLVE, Pirate) take into consideration the chemical composition of the structure ? Shouldn't this composition affect the expected density distributions ? My gratitude in advance for your comments and advice, Peter.
[ccp4bb] Histogram matching in DM - question
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 ? And a general question regarding density modification and RNA structure. Can statistical density modification programs (RESOLVE, Pirate) take into consideration the chemical composition of the structure ? Shouldn't this composition affect the expected density distributions ? My gratitude in advance for your comments and advice, Peter.
