[sharp-discuss] SHARP with two SAD isomorphous datasets

[Clemens Vonrhein]

Hi Jose,

On Wed, Jun 29, 2011 at 06:19:32PM +0200, Jose Arcadio wrote:
> I have two  derivatives soaked into the same platinum compound, 
> unfortunately the native is extremely non-isomorphous. The two platinum 
> soaks were scaled quite well because they are very isomorphous. I 
> already found the sites using shelx (doing SAD for both crystals 
> independently) also the hand is clear. I did this outside of the SHARP 
> pipeline. Just looking at the fractional coordinates of the sites they 
> seem to be different. I want to use SHARP to phase with both crystals, 
> but I am not sure whether the sites have the same origin.
> 
> My space group is C2221

Given the symmetry operators and the allowed origin shits, you get:

> soak 1
> 0.183571  0.783974  0.092060  Site1-1
> 0.355522  0.743103  0.105145  Site2-1
> 0.537300  0.722351  0.044651  Site3-1
> 
> soak 2
> 0.818542  0.218452  0.092027  Site1-1 (-x,-y,z)
> 0.644547  0.255127  0.108293  Site2-1 (-x,-y,z)

So soak 2 has the same top 2 sites, just with (-X,-Y,1/2+Z) symmetry
and an origin shift ot (0,0,0.5) ... right?

> How likely is that both crystals have the same sites and how can I be 
> sure that the sites have the same origin? Is there a way in which I can 
> use autoSHARP in order to do two SAD experiments with no native? Maybe 
> submit a MAD experiment?

You could try MAD with 2 wvl and give your 3 sites as a
sharpfiles/datafiles/xyz.hatom file:

ATOM Pt 0.183571  0.783974  0.092060
ATOM Pt 0.355522  0.743103  0.105145
ATOM Pt 0.537300  0.722351  0.044651

However, I would also just run two autoSHARP SAD runs (again with the
same 3-site *.hatom file) separately ... mixing different soaks can be
sometimes problematic.

Otherwise: use SHARP with a hierarchy like this

  C-1
    X-1
      W-1
        B-1
    X-2
      W-1
        B-1

so that you use the same 3 sites, but (because you define two
crystals) you let the HAT_OCC and HAT_B refine independently for the
two soaks.

Cheers

Clemens

PS: I'd be interested to hear what works and what doesn't of those
approaches ...

> 
> 
> Thanks a lot for all your help
> 
> Jose Arcadio Farias Rico
> PhD Student
> Höcker Group (Protein Design)
> http://www.eb.tuebingen.mpg.de/research-groups/birte-hocker/protein-design
> MPI for Developmental Biology, Spemannstr. 35, 72076 Tübingen, Germany
> Tel: +49 7071 601 365
> Fax: +49 7071 601 305
> E-Mail: jose.farias at tuebingen.mpg.de
> _______________________________________________
> 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)
***************************************************************