On 5/24/2011 2:35 AM, [log in to unmask] wrote:
> 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
If you choose your contour level based on the map rms (often inappropriately
called "sigma") the 2Fo-Fc density of a high-solvent-content map will appear
stronger even when the absolute quality is the same. All that flat space
will cause the overall rms to be low even if the rms calculated over the
protein is the same.
Dale Tronrud
> 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:[log in to unmask]] On Behalf Of
> Clement Angkawidjaja
> Sent: Tuesday, May 24, 2011 11:19 AM
> To: [log in to unmask]
> 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, [log in to unmask] 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
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