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Re: [ccp4bb]: REFMAC Vs CNS SigmaA maps



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On Fri, 8 Mar 2002, Paul Hubbard wrote:

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>
> Hello all,
>
> I have been looking at improving the current map I have made from
> MIR/MAD phases. Having traced 35% of the structure, I thought I'd give
> SigmaA a try. I did the following:
>
> REFMAC (5):
> 1) Rigid body refinement using 25 chains (secondary structure)
> 2) Restrained refinement
> 3) Calculated and viewed the SigmaA weighted maps
>
> CNS:
> 1) Rigid body refinemnet using 25 chains (secondary structure)
> 2) Simulated annealing
> 3) Calculated and viewed the SigmaA weighted maps
>
> My question is, why does REFMAC seems do have done such a good job of
> the mFo-Fc map, whereas in CNS the map looks like junk? I've compared
> the REFMAC mFo-Fc map with the original Fo map with MIR/MAD phases,
> looking at regions I suspected were secondary structure but didn't model
> in, and it suggests that there is little bias as these regions are
> improved. Could I have fallen into a trap, and CNS is giving me the
> right answer?

I am just wondering what you did with bulk solvent correction. Did you
in/exclude it out in both cases, and what about the Babinet correction in
Refmac, was that switched on or off. In such cases, would it help to include a
bulk solvent mask based on the solvent flattening mask from the experimental
phases?

Bart


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