[sharp-discuss] DM output cards

Yi Xue yi-xue at northwestern.edu
Tue Apr 10 16:18:52 BST 2007


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
>
>
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