[sharp-discuss] HL from partial model

[Clemens Vonrhein]

Hi Raj,

there are two ways of combining a partial model with SHARP
experimental phasing:

  1. include the HLs during Heavy atom refinement/phasing in SHARP

  2. include model during density modification


The most important issue is, that the MR model and your heavy atom
model need to be on the same origin and (obviously) in the same
hand. So you either

  - place the model into your SAD density

  - check/find your HA sites using phases from the MR model

Both options will make sure HA sites and MR model are consistent.

 -----------------------------------------------------------

You can calculate HLs from a model in a variaety of ways. The easiest
is to

  - place your MR solution into sharpfiles/datafiles/model_SomeThing.pdb

  - from the SHARP logfile of your best SAD run, got to the Phase
    Improvement Panel

  - there should be an option to calculate the HLs (and glue them to
    the initial MTZ file) at the bottom of the page. You might need to
    specify yourself as expert user and/or run at least one density
    modification job.

  - when starting another SHARP run, select this newly created MTZ
    file. At the bottom of the General page (in the SHARP SIN file
    editor) you can select at which stages to use these. Since it is
    independent, you can use them throughout.

 -----------------------------------------------------------

Even simpler is to use the MR model during density modification. After
(again) placing the file into
sharpfiles/datafiles/model_SomeThing.pdb, you should be able to see it
in the Phase Improvement panel. Just specify to include it (for 10, 20
or all cycles) in the density modification procedure. Check the CC you
get for the model (this will tell you it it is indeed correctly placed
with origin etc).


Hope that helps

Cheers

Clemens




On Tue, May 24, 2005 at 09:56:29AM -0400, Rajiv Chopra wrote:
> Hi ,
> I'd like to get partial phases from a MR solution to add to some iodine
> SAD data. The manual suggests that the phase improvement panel is
> capable of doing this. How do I access this panel such that the
> generation of HL coefficients is a choice? What is the best way to
> combine these phases in sharp?
> Raj
>  

> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss at globalphasing.com
> http://www.globalphasing.com/mailman/listinfo/sharp-discuss


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