Re: [ccp4bb]: REFMAC Vs CNS SigmaA maps

[Paul Hubbard <phubbard@post.its.mcw.edu>]

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Thanks for the response. I switched off bulk sovent correction in CNS as model
completeness is so low (isn't that right, since the model is used to make the
mask? - now I see your point about the solvent flipping mask). I've tried without
bulk solvent scaling in REFMAC (I assume this is the same as correction -
therefore the same reason for not including it). I thought that Babinet's
correction was the same as Bulk solvent correction.

AGS

Bart Hazes wrote:

> On Fri, 8 Mar 2002, Paul Hubbard wrote:
>
> > ***  For details on how to be removed from this list visit the  ***
> > ***          CCP4 home page http://www.ccp4.ac.uk         ***
> >
> > 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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--
Paul Hubbard
Dept. of Biochemistry
Medical College of Wisconsin
Phone: 414-456 4305
Fax: 414-456 6510
URL: iris9.biochem.mcw.edu