On Thu, May 08, 2008 at 07:26:40AM +0530, Raja Dey wrote:
> 3. Run SHARP/AutoSHARP with Se
Just run autoSHARP in SIRAS mode: you have a native and a derivative
(Se). autoSHARP is clever enough to then assign those special Se-S
atoms to you derivative, see the explanation at
http://www.globalphasing.com/sharp/manual/chapter2.html#MADnative
which is for MAD and SHARP, but you'll get the idea also for
autoSHARP.
This way you get the anomalous and 'isomorphous' differences as
signal.
> sites upto DM. Then run solvent flattening with model component 1.
What do you mean with "model component 1"? Did you include your curent
model into the density modification step (good idea)? For how many
cycles - and what was the initial CC for the model here?
If your anomalous signal of the Se is very weak and borderline you
could try and use the model phases as a restraint in SHARP during
refinement and LLG map calculation (not for the phasing step!). There
are tools in SHARP for that as well.
Another trick I use quite often is to estimate the anisotropic
B-factor of your data (reference dataset in SHARP jargon): this would
take out any anisotropy that you have, leading to more isotropic maps
going into density modification - and that could make a lot of
difference, since most real-space modificaitons in density modifcation
assume some normal shape for electron density (or at least could be
thrown off by severe anisotropy). But you have to be careful when
dealing with low-resolution data and/or incomplete data (wedges
missing etc).
Let me know if you need additional info ...
Cheers
Clemens
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