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Dear Ian,
there is one significant difference between SigmaA (PARTIAL option)
and SigmaA (COMBINE option): the latter includes experimental phases
(i.e. from heavy atom experiment). So you have for the SIGMAA program
(trying to give a tabular overview):
PARTIAL COMBINE
a) b) c) d) a) b) c) d)
input : FP SIGFP FP SIGFP
FC PHIC FC PHIC
PHIBP WP
output: FP SIGFP FP SIGFP
FC PHIC FC PHIC
PHIBP WP
DELFWT DELFWT PHDELFWT
FWT FWT PHFWT
WCMB PHCMB WCMB
where a) = amplitude
b) = sigma(amplitude)
c) = phase
d) = weight
I can't see any superfluous phase columns for the COMBINE option:
PHIC = model
PHCMB = model + experimental phase PHIBP
PHDELFWT/PHFWT = phase for calculation of 2mFo-DFc and mFo-DFc maps
and these are different things.
Same seems to be for REFMAC:
- PHIC is model (without any FPARTi, but with bulk solvent (?) I guess)
- PHWT/PHDELWT for maps
- PHCOMB if experimental phases were used
The naming of columns in SIGMAA and Refmac (same for SHARP/autoSHARP
and BUSTER-TNT btw) always tries to make it easy to 'spot' the Fourier
coefficients: FWT/PHWT, 2FOFCWT/PH2FOFCWT, FB/PHIB,
FBshasol/PHIBshasol etc. It is (as you said) _very_ easy to play
mix-and-match with values: pick any amplitude and some phase ... oh,
and while we're at it: add some weight as well (even if the amplitude
is already weighted)! My recommendation:
In 95% of cases there will be two adjacent columns in the MTZ file
(use mtzdmp to look at it) with one being of type 'F' (amplitude)
and another of type 'P': these will give the correct map.
The only 'outlier' here is SIGMAA (PARTIAL option): since only a
single phase is available (PHIC) no new PHFWT is created (since it
would be a copy of PHIC). I guess this shows the 'history' of the
program when we needed to save as much disk space as possible ... But
then: most of the time we look at maps coming out of a refinement
program and not something that's missing any anisotropic scaling, bulk
solvent correction etc ...
Cheers
Clemens
On Fri, Oct 21, 2005 at 01:19:34PM +0100, Ian Tickle wrote:
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>
>
>
> Just recently a novice user asked me why SigmaA (COMBINE option) and
> Refmac both output 3 phase columns, whereas SigmaA (PARTIAL option)
> outputs only 1. I must say I couldn't come up with a convincing answer!
> (it's always the novices that ask the really challenging questions!).
> After all there's only one set of phi(calc)'s, so why isn't there just a
> single PHIC column? SigmaA(COMBINE) and Refmac change the sign of
> negative Fourier coefficients 2mFo-DFc & mFo-DFc, and shift the
> corresponding phases by pi. SigmaA(PARTIAL) doesn't bother, it just
> outputs 2mFo-DFc, mFo-DFc & phase as calculated.
>
> The downside of this (and I can't think of an upside!) is that it
> confuses people who are trying to understand what's going on, and it's a
> recipe for making mistakes & choosing the wrong phase column. I think
> it would be entirely reasonable for someone who had just used the MTZ
> output from SigmaA(PARTIAL) to compute maps using FWT/PHIC &
> DELFWT/PHIC, to then expect to do the same thing using the outputs from
> SigmaA(COMBINE) & Refmac.
>
> Clearly getting rid of the 2 superfluous phase columns is not an option
> as it would break the scripts, but one way would be to write the 3 phase
> columns all with the same phase, but with existing columns labels, then
> whichever phase column you chose you would be right! - and I don't think
> anyone would notice!
>
> Anyone got any thoughts?
>
> -- Ian
>
> ********************************************
> Ian J. Tickle, DPhil.
> Director of X-ray Technology
> Astex Therapeutics Ltd
> 436 Cambridge Science Park
> Milton Road, Cambridge
> CB4 0QA, UK
> Tel: +44(0)1223 226214
> Fax: +44(0)1223 226201
> www.astex-therapeutics.com
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