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> -----Original Message----- > From: Clemens Vonrhein [mailto:[EMAIL PROTECTED] > Sent: 21 October 2005 15:26 > To: Ian Tickle; CCP4 Bulletin Board > Subject: Re: [ccp4bb]: Phase columns in SigmaA & Refmac. > > Dear Ian, > > now I see what you want (my inital reply didn't go through to ccp4bb > ... yet ... seems to happen to me on a regular basis). > > I think the problem might be definitions: in $CCP4/doc/mtzformat.doc > you see that a column of type 'F' is a 'structure amplitude' (should > probably read 'structure factor amplitude'. And according to > http://en.wikipedia.org/wiki/Amplitude, 'Amplitude is a nonnegative > scalar'. > > So to have non-negative amplitudes we need to change the phase, which > (again $CCP4/doc/mtzformat.doc) is 'phase angle in degrees' (no > restrictions here, although something like '0 <= x < 360' > _or_ '-180 <= > x < 180' might be good. Hi Clemens Again this is a question of whether adhering to a convention merely for its own sake provides you with some benefit, or whether it causes you pain! As Kevin said "arguably this is a dumb convention". > So it is possible that a lot of MTZ reading programs will give you > problems if they encounter a negative F column. As pointed out SigmaA(PARTIAL) uses a single phase for both FWT & DELFWT, and therefore must output -ve amplitudes (which can be confirmed by looking at the MTZ file). AFAIK SigmaA has been used for years without causing problems with other software! The reason is simply that checking the value of F only occurs if an associated sigma(F) column is present, which is not the case here. > > Obviously, we could avoid all this by giving two reals (column type > 'R') for map calculation: the real and imaginary part of the structure > factor. But then applying a weight is a bit more messy (if it needs to > be applied) ... Oh dear! > > It looks to me as a case of 'if it ain't broke don't fix it' - but > with some effort in clarifying documentations. I would say it's more of a case of "it's broken so fix it!" - particularly if fixing it has no side-effects (what more could you ask for?). Cheers -- Ian ********************************************************************** CONFIDENTIALITY NOTICE This email contains confidential information and may be otherwise protected by law. Its content should not be disclosed and it should not be given or copied to anyone other than the person(s) named or referenced above. If you have received this email in error, please contact [EMAIL PROTECTED] **********************************************************************
