Dear Herman, You are right. Thank you for the explanation.
Clement > Dear Clement, > > In case of a noisy experimental map, you have to do explicit solvent > flattening. However, in case of molecular replacement, if the model > occupies only say 30% of the asymmetric unit, the solvent where there is > no model, will be flattened automatically. You can also view it like > this: if 70% of the asymmetric unit is featureless solvent, the model at > hand (=flat bulk solvent model), will be very accurate. I never really > tested this, but in the cases where I had a very high solvent content, I > was always surprised by the quality of the electron density maps. Off > course, crystals with a high solvent content tend to diffract poorly and > if the solvent is not featureless, this will not work either. > > If you get high Rfree values for a structure with high solvent content, > I would get suspicious and look for extra molecule(s), which may have > been overlooked. If these extra molecule(s) are disordered, this will > off course lead to high Rfree values. > > Best, > Herman > > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > Clement Angkawidjaja > Sent: Tuesday, May 24, 2011 11:19 AM > To: [email protected] > Subject: Re: [ccp4bb] how to remove part of data with bad signal to > noise ratio > > But you have to do solvent flattening (density modification), which > people often (unintentionally?) skip for structures solved with > molecular replacement. Please correct me if I am wrong. > > Clement > > On May 24, 2011, at 6:01 PM, [email protected] wrote: > >> This is not my experience. Provided the solvent is featureless, I find > >> that a high solvent contents leads to a lower Rfree due to a kind of >> solvent flattening effect. Of course, if a significant part of the >> molecule(s) is/are disordered, this will lead to a degradation of the >> Rfree. >> >> My 2 cents, >> Herman >
