[sharp-discuss] DM output cards

[Clemens Vonrhein]

Dear Yi,

yes, you should always use the best map for model building (either by
hand on the graphics or with automatic tools like ARP/wARP etc).

However, I thought your question was about restrained refinement 9and
not model building)? If you want to add experimental phase information
as a restraint to your model refinement you need to be aware that
those phase restraints will be used in the form of (phase)
probabilities: and you can only combine different probabilities if
they're independent. Also, phase probabilities after density
modification (at least using the methods in SHARP/autoSHARP - DM and
SOLOMON, i.e. 'classical' density modification) will lead to an
over-estimate of the accuracy of those phases.

Summary:

  for maps: use best amplitude/phase for calculating the map
  (e.g. FBshasol/PHIBshasol from eden_flat*.mtz)

  for refinement: use HLA-D from eden.mtz

Cheers

Clemens

On Tue, Apr 10, 2007 at 10:18:52AM -0500, Yi Xue wrote:
> Dear Clemens:
>    If we only use the pure SHARP phases, what is the point of doing density
> modification? (only for finding the right hand in SIR, SAD cases?) Sorry for
> another stupid question. I always thought we should use the 'improved' map
> to start the model building after solvent flattening.
> 
> best
> Yi
> 
> 
> 
> -----Original Message-----
> From: Clemens Vonrhein [mailto:vonrhein at globalphasing.com]
> Sent: Tuesday, April 10, 2007 1:44 AM
> To: Yi Xue
> Cc: sharp-discuss at globalphasing.com
> Subject: Re: [sharp-discuss] DM output cards
> 
> 
> Dear Yi,
> 
> use FPsha, SIGFPsha and as phase restraints HLA-HLD. Always use
> Hendrickson-Lattmann coefficients as experimental phase information -
> and use the pure SHARP phases, not some phases from density
> modification (which will be overestimated).
> 
> As Kevin said: the information is a 'bit' burried ...
> 
> Cheers
> 
> Clemens
> 
> On Mon, Apr 09, 2007 at 01:45:59PM -0500, Yi Xue wrote:
> > Dear all:
> >
> >        Sorry for the stupid question.  I am new to sharp/autosharp. I ran
> a
> > heavy atom refinment job in autosharp, and feed the refined heavy atom
> sites
> > into the DM in sharp. The heavy atom sites are present in the crystals as
> > cofactors, not derivatives. The output eden_flat_##.#pc.mtz contains a lot
> > of F*, PHI* cards.  My next step is to start the restrained refinement, I
> am
> > a little confused which Fp, sigma, and Phi, FOM should I input?
> >
> > Here is the whole list of the cards:
> >
> > H K L Fcentsha PHIcentsha FOMsha HLA HLB HLC HLD FHsha PHIHsha FreeR_flag
> > FPsha SIGFPsha Fcentshasol PHIcentshasol FBshasol PHIBshasol PHIshasol
> > FOMshasol FCshasol PHICshasol PHIdm FOMdm Fdm HLAdm HLBdm HLCdm HLDdm
> >
> > I would appreciate if anyone could help to give me some ideas about what
> are
> > the differences between F* cards, or send me some links for explanations
> of
> > them.
> >
> > Best
> > Yi
> >
> >
> > _______________________________________________
> > sharp-discuss mailing list
> > sharp-discuss at globalphasing.com
> > https://www.globalphasing.com/mailman/listinfo/sharp-discuss
> >
> 
> --
> 
> ***************************************************************
> * 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)
> ***************************************************************
> 

-- 

***************************************************************
* 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)
***************************************************************