Clemens - what do you mean by "correcting anisostropy"?
On 28/01/2015 07:42, Clemens Vonrhein wrote:
> Dear Nicolas,
>
> On Mon, Jan 26, 2015 at 03:21:00PM +0000, Nicolas Soler wrote:
>> A quick question regarding the density modification interface via
>> the Sharp interface. Which resolution range / radius of the solvent
>> sphere/ ncycles should be used for optimal result?
> I usually don't play around a lot with those parameters - other than
> possibly increasing the number of cycles to something like 100.
>
>> The documentation seems to suggest to restrict yourself up to the
>> resolution where good phasing information is available (6.5A in my
>> case) and I get excellent indicators only if I do that (they become
>> horrible if I use the full resolution range).
> Going from low resolution phase information (say below 4-4.5A) to the
> high resolution limit of your data (even if that is 'only' 3A) is
> notoriously difficult when doing 'only' solvent flattening or
> flipping. To get over that bump, NCS-averaging would be a massive
> help. Or if you have some initial model - maybe a partial MR solution
> or such - you can add this to the mix as well.
>
> The other thing about such low-resolution phase information or data is
> that a lot of the statisitical indicators can become rather noisy and
> much less reliable.
>
> Your statistics will automatically be much worse if you include higher
> resolution data, since you will have many more reflections with poor
> initial phase information going into the same, single value. The
> important thing: do the maps look better than if you use only
> low-resolution data all the way through?
>
>> How about phase extension ? Which parameters would you then use?
> Maybe somebody else has more experience with fine-tuning those
> parameters. For me the some other important things are happening a
> step before that density-modification:
>
> * do the two hands/enantiomoprhs show a significant difference in
> score?
>
> * is the HA model as complete and accurate as possible (using the LLG
> maps in SHARP for checking)?
>
> * is there severe anisotropy in your data? This can be a real pain for
> the density-modification and you should try to correct for it before
> doing any density-modification procedure if possible.
>
> Cheers
>
> Clemens
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