Dear Gerard, Thank you so much for letting us know of the reference and details about your long-standing BUSTER method for ligand density maps which we now see is very similar to our recent polder map method. We apologize for not being aware of the early reference and we will be very sure to cite it in future publications. Very best regards, Pavel
On Thu, Feb 16, 2017 at 5:35 AM, Gerard Bricogne <g...@globalphasing.com> wrote: > Dear Pavel, > > As much as I would have wished to, I was unable to contribute to > this thread for the past week because of more pressing matters. I hope > it hasn't entirely gone cold in the minds of CCP4BB readers. > > I want to congratulate the Phenix developers for having come up > with such a catchy name for a method that was first conceived, and > implemented in autoBUSTER, by Clemens Vonrhein over 12 years ago, and > has been abundantly exercised and appreciated for its usefulness by > its users (especially, drug discovery companies) ever since. > > You do mention BUSTER: > > The program BUSTER (Bricogne et al., 2016) allows the exclusion of > regions from bulk solvent by processing an additional file which > describes the binding site (without resembling the putative ligand). > Furthermore, statistical treatment of non-uniformity of bulk solvent > or as yet unmodeled regions has been discussed ... [with two more > BUSTER-related references dated 2000 and 2004] > > but the 2016 date (which is the one we recommend that users cite for > the latest version of the program) rather obliterates any sense of > chronology when it comes to the specific underlying idea of "Polder > maps" and of its prior implementation mentioned above. > > We (here) can certainly not claim to be champions when it comes > to publicizing our work through the usual channel of polished academic > publications, as our lives as developers are driven and dominated by > rather different imperatives. However there happens to be an official > record of the origins of that method in > > http://journals.iucr.org/a/issues/2005/a1/00/a32958/a32958.pdf > > or (for a prettier format) > > http://dx.doi.org/10.1107/S0108767305089415 > > To complete that record: this development was released to our > Consortium members in November 2003, and to academic users at large in > July 2009. It is described in quite explicit terms in the online > documentation we later wrote for academic users and posted on our > external Wiki, e.g. > > http://web.archive.org/web/20121216164211/http://www. > globalphasing.com/buster/manual/autobuster/manual/autoBUSTER5.html > > In spite of the lack of a standard academic reference, this > feature has therefore been an open secret for a very long time under > the name of "the -L option" in autoBUSTER, where L stands for "ligand > chasing". > > > So, again, congratulations for finding such a good name for the > method and for publishing a collection of nicely illustrated examples > of its usefulness. Your presentation, however, might be seen as rather > economical in its acknowledgment of "prior art" - a notion that surely > has to be recognised as existing outside the confines of standard, > neatly packaged, immediately quotable Acta D publications :-) . > > > With best wishes, > > Gerard. > > -- > On Thu, Feb 09, 2017 at 03:45:22PM -0800, Pavel Afonine wrote: > > In addition to excellent Kay's reply.. > > > > Also make sure to check refined B factors. Note, if the ligand is not > there > > then that volume is likely filled with bulk-solvent. Now low occupancy in > > combination with very large B factors may approximate bulk-solvent quite > > well. The Polder map along with three CC values that its calculation > > procedure reports should give you the answer whether the ligand is there > or > > not. > > > > Pavel > > > > On Wed, Feb 8, 2017 at 2:43 AM, Kay Diederichs < > > kay.diederi...@uni-konstanz.de> wrote: > > > > > Dear Petr, > > > > > > if I understand correcty, the mFo-DFc density (1) shows almost > nothing, > > > but the 2mFo-DFc (2) as well as the composite omit map (3) show the > ligand? > > > > > > As you say, the apparent contradiction between (1) versus (2)&(3) is > > > unexpected. One explanation could be that the Fc are simply too bad, > i.e. > > > the model not good enough to result in useful signal in the difference > > > map. OTOH, that you see the ligand in (2) may be simply model bias, > so is > > > not meaningful. (3) is hopeful since there is no model bias. > > > > > > I would suggest to > > > - refine the occupancy, to find out why the density is so weak > > > - calculate a (Fo,soak - Fo,native) (4) map with phases from a model > > > unbiased by the ligand > > > - try a Polder map (5) > > > > > > - If the occupancy is around 0.5 or higher, that would be a good sign. > > > - but if you don't see density in (4) and (5), then your ligand is > > > probably not there in any useful amount > > > > > > I consider (4) as the most sensible method to show presence of the > ligand, > > > and it should convince reviewers. > > > > > > HTH, > > > > > > Kay > > > > > > > > > > > > On Wed, 8 Feb 2017 09:05:50 +0100, Petr Kolenko < > petr.kole...@fjfi.cvut.cz> > > > wrote: > > > > > > >Dear colleagues, > > > > > > > >we have a dataset with potential enzyme:ligand complex at 2.2 AA > > > >resolution. The ligand is very good substrate for the enzyme, we used > > > >soaking. We do not see the ligand in the regular difference electron > > > >density, only five out of twenty atoms. However, the ligand placed at > > > >the active site (model used from structure of a mutant variant) is > > > >refined well, giving no negative peaks in difference electron density > > > >map and nice observed electron density. I have calculated composit > omit > > > >map with annealing in Phenix (input model did not contain the ligand) > > > >and the electron density for the ligand is there. > > > > > > > >I have my own opinion, but we are desperate to obtain such data (more > > > >than 40 crystals already tested). My question is, would this be proof > of > > > >presence of the ligand with reduced occupancy? Will this map convince > > > >the reviewers? Is there any other way to validate presence of the > ligand? > > > > > > > >Best regards, > > > >Petr > > > > > -- > > =============================================================== > * * > * 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 * > * * > =============================================================== >
