Hi, A map from phenix.refine is probably better, if you're going to choose one, for two reasons: 1. As you say, it includes a proper bulk solvent contribution. 2. Phaser doesn't (at least yet -- we might get around to putting it in some day) refine the Sigma(A) values, so the weights are determined from the guesses about the RMS error of the model. I think Phaser usually does a pretty good job of rigid-body refinement, but it shouldn't hurt to repeat this step in phenix.refine. If there are any domains that might move, this would be a good time to refine them as separate rigid bodies. Regards, Randy Read On Aug 30 2009, Pavel Afonine wrote:
Hi Peter,
I guess this my reply will not replace Tom's or Randy's one...
Should it be the 2mFo-DFc map directly from Phaser or would it be better to do rigid body refinement in phenix.refine and use the bulk solvent corrected 2mFo-DFc map ?
- why don't you try using both options and choose the best outcome?
- running a round of rigid body refinement in phenix.refine and using its 2mFo-DFc map will not hurt at least or may make your model and therefore the map better, so you will have a better starting point.
Pavel.
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