RE: [ccp4bb]: ArpWarp Mode Solvent

[Petrus Hendrik Zwart <Zwart@embl-hamburg.de>]

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> Is is best to use experimental phases for 'mode solvent', ie  
> 
> Always -- unless your phases REALLY suck, I guess.  Not using phases is
> like chucking half of your observations.  (Well, maybe not EXACTLY half.
> But it's the idea that counts.) 

Interesting point.

In principle, all prior information should be usefull during refinement. 
In practice, I have no clue if experimental phases will add much information 
when you are allready in the position that you can add waters (unless you
phases are extremely good i guess). Besides that, one has to be sure that
the HLC's are okai. 
Was this particular case an (M/S)(IR/AD) or MR model?


I guess there are some people out there that have some answers based on
experience in stead of 'gut-feelings' ... 

The fine manual says on this point:

/*-----------------------------------------------------------------------*/
Do you plan to use experimental phases as input (i.e. for mode warpNtrace
or warp) (Y/N) ? Y 
Amplitude (weighted) for initial map calculation: FSE1 
Phase for initial map calculation: PHIDM_123p 
FOM. Press <Enter> if amplitude is already weighted : FOMDM_123p 

First the number of residues in the asymmetric unit is entered. Since we
want to start from experimental phases the answer was Y. 

>> Answering with N
   means that you are interested in either starting from a
   molecular replacement solution, building the solvent of a refined
   structure or trying the ab initio option.  <<

/*-----------------------------------------------------------------------*/




Protocol wise, I would choose W or write my own script so one
can tweak around a bit more because (I_hate_automated_scripts option).



Peter