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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. So it is possible that a lot of MTZ reading programs will give you problems if they encounter a negative F column. 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. Cheers Clemens On Fri, Oct 21, 2005 at 03:11:14PM +0100, Ian Tickle wrote: > > -----Original Message----- > > From: Clemens Vonrhein [mailto:[EMAIL PROTECTED] > > Sent: 21 October 2005 14:37 > > To: Ian Tickle > > Subject: Re: [ccp4bb]: Phase columns in SigmaA & Refmac. > > > > Hi Ian, > > > > I just realised that I might have misunderstood your remark: you want > > to have more columns in the MTZ file and not 'getting rid of the 2 > > superfluous phase columns'? So are you concerned with the SigmaA > > (PARTIAL option) being wrong? > > > > Cheers > > > > Clemens (confused by the last two messages ... that came after I > > answered) > > > Hi Clemens > > No my suggestion is to have exactly the same number of columns as now > with identical labels. However phase columns which carried the same > info would contain identical values. I think in the case of Refmac only > 2 columns, not 3, carry the same info: PHWT & PHDELWT; PHIC doesn't > include the solvent contribution so it will be different. > > As an aside, arguably FC/PHIC should contain the solvent contribution > (in which case the PHIC column will be redundant), since we use it to > compute Fc maps for real-space density correlation with 2mFo-DFc maps > and ideally we should be correlating estimates of the same thing! > > I don't agree that there's no redundancy: in SigmaA(COMBINE) PHCMB, > PHFWT & PHDELWT are all the same phase before being shifted because of > -ve amplitude, and similarly one of PHWT & PHDELWT is redundant in > Refmac. Of courser redundancy isn't the issue, it's the potential for > making mistakes that's important. > > Here's an example from a Refmac output MTZ file: > > NOW > === > H K L FreeR_flag F SIGF FC PHIC FWT > PHWT DELFWT PHDELWT FOM > > 1 3 1 9.00 419.24 14.61 689.35 356.32 61.66 > 349.81 189.62 169.81 0.60 > > 1 3 2 14.00 677.57 19.02 154.17 328.72 181.24 > 118.08 57.65 118.08 0.18 > > 1 3 4 8.00 996.96 26.22 683.30 326.94 1212.98 > 323.20 323.31 323.20 0.89 > > > MY SUGGESTION > ============= > > H K L FreeR_flag F SIGF FC PHIC FWT > PHWT DELFWT PHDELWT FOM > > 1 3 1 9.00 419.24 14.61 689.35 356.32 61.66 > 349.81 -189.62 349.81 0.60 > > 1 3 2 14.00 677.57 19.02 154.17 328.72 -181.24 > 298.08 -57.65 298.08 0.18 > > 1 3 4 8.00 996.96 26.22 683.30 326.94 1212.98 > 323.20 323.31 323.20 0.89 > > > Focus on the FWT, PHWT, DELFWT & PHDELWT columns. In the 1st case the > F's are all +ve and the PHWT & PHDELWT are in general different. In the > 2nd case, some F's are -ve but the PHWT & PHDELWT columns are identical > (so it doesn't matter which you choose). These datasets will of course > produce identical maps! > > 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] > ********************************************************************** > Content-Description: m.dat > [-- octet-filter file type: "ASCII text" --] > > H K L FreeR_flag F SIGF FC PHIC FWT > PHWT DELFWT PHDELWT FOM > > 1 3 1 9.00 419.24 14.61 689.35 356.32 61.66 > 349.81 189.62 169.81 0.60 > > 1 3 2 14.00 677.57 19.02 154.17 328.72 181.24 > 118.08 57.65 118.08 0.18 > > 1 3 4 8.00 996.96 26.22 683.30 326.94 1212.98 > 323.20 323.31 323.20 0.89 > > > H K L FreeR_flag F SIGF FC PHIC FWT > PHWT DELFWT PHDELWT FOM > > 1 3 1 9.00 419.24 14.61 689.35 356.32 61.66 > 349.81 -189.62 349.81 0.60 > > 1 3 2 14.00 677.57 19.02 154.17 328.72 -181.24 > 298.08 -57.65 298.08 0.18 > > 1 3 4 8.00 996.96 26.22 683.30 326.94 1212.98 > 323.20 323.31 323.20 0.89 Content-Description: m.dat > [-- octet-filter file type: "ASCII text" --] > > H K L FreeR_flag F SIGF FC PHIC FWT > PHWT DELFWT PHDELWT FOM > > 1 3 1 9.00 419.24 14.61 689.35 356.32 61.66 > 349.81 189.62 169.81 0.60 > > 1 3 2 14.00 677.57 19.02 154.17 328.72 181.24 > 118.08 57.65 118.08 0.18 > > 1 3 4 8.00 996.96 26.22 683.30 326.94 1212.98 > 323.20 323.31 323.20 0.89 > > > H K L FreeR_flag F SIGF FC PHIC FWT > PHWT DELFWT PHDELWT FOM > > 1 3 1 9.00 419.24 14.61 689.35 356.32 61.66 > 349.81 -189.62 349.81 0.60 > > 1 3 2 14.00 677.57 19.02 154.17 328.72 -181.24 > 298.08 -57.65 298.08 0.18 > > 1 3 4 8.00 996.96 26.22 683.30 326.94 1212.98 > 323.20 323.31 323.20 0.89 -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************
