[sharp-discuss] phase combination MAD and MIR

Ditlev Egeskov Brodersen deb at bioxray.dk
Wed Nov 2 07:39:54 GMT 2005


 Hi Sabine,

  in this case I would simply create a standard MAD setup with SHARP for
your Fe data, and then add the Pt data at a separate COMPOUND level, but
without any G- or C-SITEs. When you do this, you will only get phasing from
the Fe-sites that you trust, but retain the possibiliy of calculating
residual maps against the Pt-data to properly locate new sites. This can be
done automatically by SHARP after the first phasing run, and you can keep
going until there are no more sites to find.

  Regarding refinement parameters, it's VERY important to refine the
NONISOMORPHISM PARAMETERS for the second data set (Pt), otherwise the
phasing won't work.

Regards,

  Ditlev

---

Ditlev E. Brodersen, Ph.D.
Lektor, Associate Professor

Department of Molecular Biology   Office:  +45 89425259
University of Aarhus              Lab:     +45 89425022
Gustav Wieds Vej 10c              Fax:     +45 86123178
DK-8000 Aarhus C                  Email:   deb at bioxray.dk
Denmark                           Lab WWW: http://bioxray.dk/~deb

 


-----Original Message-----
From: sharp-discuss-bounces at globalphasing.com
[mailto:sharp-discuss-bounces at globalphasing.com] On Behalf Of Sabine
Schneider
Sent: 1. november 2005 20:43
To: sharp-discuss at globalphasing.com
Subject: [sharp-discuss] phase combination MAD and MIR

Hi everyone,

I have a Fe-MAD data set with weak phases and I want to combine it with a
platinum derivative. 

How can I best combine these two in SHARP if I do not have the platinum
sites (the fe site I have seems to be clear), so I can not specify the
G-sites for PT in the SHARP input? From the difference patterson it seems
that I have
3 Pt sites. 
Is it for example a good idea to use the phases of the iron and set the
G-sites for the Pt to xyz all to 0.1, occ 1 and let SHARP refine these? Or
how do I best tell SHARP to use the fe MAD phases to go "hunting" for the
pt?

And what refinement flags are best set to start with?

Thanks a lot 

Sabine





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