While not entirely CCP4 based, my question is addressed to those who have successfully used ArpWarp for solvent building. Our model has R/Rfree of about 24.5/28.5 to 2.2 Angstroms resolution with no solvent built.
Is is best to use experimental phases for 'mode solvent', ie
Always -- unless your phases REALLY suck, I guess. Not using phases is like chucking half of your observations. (Well, maybe not EXACTLY half. But it's the idea that counts.)
[Do you plan to use experimental phases as input (i.e. for mode warpNtrace or warp) (Y/N) ? Y]
Secondly, any suggestions on which REFMAC protocol is most appropriate in our case (shown below)? I would assume either 'R' or 'W' but was curious if anybody has previous experience with others.
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You can choose between the following REFMAC protocols:
F A fast protocol that works with good data.
S A considerably slower one which might work better in difficult cases.
R The slow protocol together with Rfree.
P Phased maximum likelihood refibement.
O The good old SFALL ...
H Optimised parameters for starting from heavy atoms alone.
W Optimised parameters for solvent building.
A Advanced mode for setting parameters manually.
What is your choice ? (F/S/R/P/O/H/W/A) W
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P: phased refinement.