Re: [ccp4bb]: REFMAC Vs CNS SigmaA maps

[<jyl@mrc-lmb.cam.ac.uk>]

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Paul,

could it be that you forgot to combine the MIR/MAD and model phases
in CNS ? Besides using HL's and mlhl in the refinement, you also have to
use 'combined' in the map calculation. Also, simulated annealing on many
small stretches of residues might not be such a good idea...

Good luck,
Jan


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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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