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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Clement Angkawidjaja Sent: Tuesday, May 24, 2011 11:19 AM To: CCP4BB@JISCMAIL.AC.UK 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, herman.schreu...@sanofi-aventis.com 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
