Hi Peter, yes, I would use the one after rigid-body refinement run in phenix.refine. Pavel. On 8/30/09 2:32 PM, Peter Grey wrote:

Hi Pavel,

Thank you very much for your fast answer. I just thought that maybe the bulk solvent correction procedure in phenix can really create better maps because with such big complexes I must use all low resolution data. Of course I can try both options but there are so many things to try with this big complex at low resolution that I would like to eliminate options where possible.

Many many thanks,

Peter.

On Sun, Aug 30, 2009 at 7:22 PM, Pavel Afonine mailto:[email protected]> 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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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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