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
