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Hi,
I find small differences between refmac and cns, depending on the case. The SA
omit map is a useful tool, but again it depends on the case. Don't bury CNS
(yet).
Cheers,
Boaz
>
> From: Dirk Kostrewa <[EMAIL PROTECTED]>
> Date: 2005/08/18 ה PM 12:08:15 GMT+03:00
> To: Anthony Duff <[EMAIL PROTECTED]>, CCP4BB <[email protected]>
> Subject: Re: [ccp4bb]: R-fac and R-free from mapfiles?
>
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> *** CCP4 home page http://www.ccp4.ac.uk ***
>
>
> Hi Anthony and other CCP4ers,
>
> Anthony Duff wrote:
>
> > *** For details on how to be removed from this list visit the ***
> > *** CCP4 home page http://www.ccp4.ac.uk ***
> >
> >
> > Its my experience that:
> >
> > 1. Simulated annealing, even without omitting anything, does a lot of
> > damage to a refined structure
>
> also my experience - after the first hype with SA, I'm not using it for
> many years anymore, for that reason.
>
> >
> > 2. CNS does a worse job of refining a structure in the late stages,
> > even accounting for differences in default restraint weights. (I
> > don't know why this would be so, with both using maximum likelihood...
> > maybe the CNS algorithms are inferior?)
>
> Yes, the automatically determined "wa" weights in CNS are a factor 2-3
> too small (at least in my experience). It is easy to modify the script
> for automatic weight determination, accordingly.
>
> > My current opinion is that you shouldn't bother with SA-OMIT maps when
> > your structure is done, and that an ordinary refmac omit map is good
> > enough (set q=0 for omitted atoms, do enough rounds of refinement to
> > loose bias, then look at the ordinary DELFWT map). The rationale is
> > that in the finished structure, the phases are essentially correct and
> > you have got rid of superfluous bits of model (atoms not corresponding
> > with electron density) that are able to retain memory of the omitted
> > atoms.
>
> Here, one has to be very cautious: it is generally safer to remove the
> partial structures to be omitted from the coordinate file rather than to
> set their occupancies to "0", even if the geometry at the boudaries will
> get worse. The reason lies in the bulk solvent mask: if atoms with zero
> occupancy are still considered in the bulk solvent mask calculation,
> they leave a completely empty region in that bulk solvent mask. Since
> there shouldn't be any empty region there (you will have either a more
> or less ordered part of your structure or continuous bulk solvent
> density), this empty region will show up as positive peaks in a
> difference map (positve observed density minus empty density gives
> positive peaks), thereby self-confirming what has been put in before.
> This is exactly what you don't want in an omit-map! By removing the
> atoms from the structure you avoid such holes in the bulk solvent mask.
> I've seen exactly such self-confirming peaks in CNS difference maps by
> setting the occupancies of omitted atoms to zero, instead of removing
> them, and doing a mask bulk solvent correction. But maybe REFMAC5
> ignores atoms with zero occupancy in the bulk solvent mask calculation
> (Garib?)? If yes, it would be safe with REFMAC5 to set their occupancies
> to zero, if no, better remove them from the coordinate file.
>
> Best regards,
>
> Dirk.
>
> --
>
> ****************************************
> Dirk Kostrewa
> Paul Scherrer Institut
> Life Sciences, OFLC/110
> CH-5232 Villigen PSI, Switzerland
> Phone: +41-56-310-4722
> Fax: +41-56-310-5288
> E-mail: [EMAIL PROTECTED]
> http://sb.web.psi.ch
> ****************************************
>
>
