Sorry found it: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1853337
... and it's Brian Matthews not Mathews. -- Ian > -----Original Message----- > From: [email protected] [mailto:[email protected]] On > Behalf Of Ian Tickle > Sent: 02 June 2009 10:35 > To: Ana-Maria Goncalves > Cc: Dirk Kostrewa; CCP4BB > Subject: RE: [ccp4bb] solvent mask with refmac > > The other possibility of course is that the data is good, that this is > an accurate experimental result and there really is a void, or at least > a cavity where the mean bulk density is lower than in bulk water. One > way to test the void theory would be to fill the cavity with O atoms of > zero (or very small, say 0.01) occupancy. Hopefully (!) that will > prevent Refmac filling the cavity with bulk solvent. One could then try > giving these O atoms large B factors, say 200, to smear them out, and > then increase the occupancies to titrate the actual bulk density. > > There was a paper by Brian Mathews group (sorry I don't have the > reference) on a high pressure form of lysozyme where they found a large > hydrophobic void (I think sufficient to contain something like 5 > waters). Bulk water could only be compelled to enter the void by > application of very high external pressure. > > Interesting! > > Cheers > > -- Ian > > > -----Original Message----- > > From: [email protected] [mailto:[email protected]] > On > > Behalf Of Dirk Kostrewa > > Sent: 02 June 2009 10:13 > > To: CCP4BB > > Subject: Re: [ccp4bb] solvent mask with refmac > > > > Dear Ana-Maria, > > > > in my experience, mask bulk solvent artifacts can only occur at narrow > > channels, where the mask radius is too big to define the channel as > > belonging to the bulk solvent region, leaving it "empty" and thus > > resulting in positive (!) difference density. Changing from simple > scaling > > to Babinet scaling is an important check to exclude mask bulk solvent > > artifacts, but there, you have to uncheck the "calculate contribution > from > > the solvent region", because this is done by the Babinet scaling, > already. > > However, in your case, you have negative difference density in a, as > you > > say, big cavity. This will be certainly filled with bulk solvent > density. > > One possible reason for a negative difference density are > underestimated > > magnitudes of |Fobs| at very low resolution, either because they are > > weakened by the beam-stop (half-)shadow, or because they are overloads > > that have been poorly extrapolated. A simple check for wrongly > determined > > low-resolution |Fobs| is to cut your low resolution data during > refinement > > at a somewhat higher resolution, say 20 A instead of 80 A, and see > whether > > the negative difference density disappears. If, yes, you should check > your > > data processing again. > > > > Best regards, > > > > Dirk. > > > > Am 02.06.2009 um 10:43 schrieb Ana-Maria Goncalves: > > > > > > Dear BB, > > > > I'm refining a structure which presents a big hydrophobic cavity > > where a strong residual difference negative density can be seen. I > presume > > that this is an effect of not having a proper solvent mask determined > and > > I was wondering if there is a way to provide a better mask description > to > > REFMAC. The resolution of the data is 1.6 A and I have already tried > > changing from simple to Babinet scaling, without any improvement. Any > > advice/suggestion would be very welcome. > > > > Many thanks, > > Ana-Maria > > > > > > > > -- > > Ana-Maria Goncalves > > Macromolecular Crystallography Group > > European Synchrotron Radiation Facility > > B.P. 220, 6 rue Jules Horowitz > > F-38043 GRENOBLE CEDEX > > FRANCE > > > > Tel: +33 (0) 4.76.88.19.12 > > Fax: +33 (0) 4.76.88.29.04 > > > > > > > > > > ******************************************************* > > Dirk Kostrewa > > Gene Center, A 5.07 > > Ludwig-Maximilians-University > > Feodor-Lynen-Str. 25 > > 81377 Munich > > Germany > > Phone: +49-89-2180-76845 > > Fax: +49-89-2180-76999 > > E-mail: [email protected] > > ******************************************************* > > > > > > Disclaimer > This communication is confidential and may contain privileged information > intended solely for the named addressee(s). It may not be used or > disclosed except for the purpose for which it has been sent. 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