RE: [ccp4bb]: map coefficients in Refmac and CNS

[Jorge Iulek <iulek@interponta.com.br>]

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> > 2) What is the so called phi_calc phase in CNS ? The corresponding
> > PHIC of 
> > REFMAC, that is, based solely on the model coordinates?  But, should
> > these
> > phases not bias the density towards the model and then explain why I
> > see a 
> > better density around my ligand in CNS maps ? 
> 
> Did you include your ligand in the refinement?  (Your question seems to

  As to the points I put initially, yes. But I also tried to refine omitting 
the ligand (not  putting it in the refinement programs) and , once again, 
practically the same happened ! In the Fourrier difference maps, CNS 
shows "reasonably well" the whole ligand (although little weaker - but + 3 
sigma OK at the difference Fourrier - in the regions where refmac does not show 
at all), while REFMAC does show the same density trend it shows when I input 
the ligand in the refinement, ie., density breakage and not comprising the 
whole  ligand.

> imply you did.)  If you want to decide what's in there, you should
> definitely remove whatever you *thought* was there, and judge by the
> difference density.
> 

  Yes, but the matter is that such difference densities are quite "different" 
(one from the other) as output by refmac and CNS, which I was thinkig were due 
to refmac "combined" phases PHWT and PHDELWT. So I would like to know whether 
it is always better to calculate my weighted 2Fo-Fc and Fo-Fc maps with them or 
in some situations I should use PHIC as I am supposing CNS always does ...
  Anyhow, there seems to be a good sight as the Fourrier difference in CNS show 
the "whole ligand". But why should REFMAC later on break its density ? For 
curiosity, I also fft'ed a map with FWT and PHIC (output from a Refmac run 
where I input also the ligand) and the ligand looks much better than with FWT 
and PHWT ...

> Cheers
> phx.
> 

  Thanks for your initial suggestions. More ideas and other suggestions are 
welcome.

Jorge