Re: [ccp4bb] Advice for phasing

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: pink/green paper?
From: James Murray James {- dot -} Murray {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-07-17

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Subject: Re: Advice for phasing
From: Jacob Keller j-keller2 {- at -} MD {- dot -} NORTHWESTERN {- dot -} EDU
Date: 2008-07-17

Subject: Re: Advice for phasing
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-07-17

Hi -

I would try SHARP; or to be exact be tempted to think less and use
autoSHARP with the description of all datasets and only give it the Se
sites for the seMet crystal. The same thing can also be done easily in
Solve. In both cases I would start with unmerged data and let these
programs do their nice scaling, which might be key for your case.

Now, if one crystal system is converted to another by a simple soak, I
presume they are related.
Thus, it should be trivial (*) to figure out the relationship
(transformation matrix) between the two.

As soon as you do so use DMMulti from the CCP4, the phases from the Se/
Hg phasing experiment, and the "good" native data, together with the
transformation matrix from above to do cross-crystal averaging. I
suspect that one of your crystal systems will also have some NCS (I
suspect that upon soak a crystallographic axis becomes non-
crystallograpic) which you should of course also define and use.
Presuming now, that your 'good' native is also in higher resolution I
would use then the 'native' phases to run ARP/wARP (or Resolve,
Buccanneer, ACMI; but I am biased)

A.

(*) As it has been noted before in the bb, climbing mountain Everest
is trivial. It has been done before, its being done now, and will be
done again. But it takes intense training and determination to
succeed. Same as getting the transformation between the two related
space groups. In both cases though, failure is also an option.

On Jul 17, 2008, at 17:13, Junyu Xiao wrote:

> Hi,
>
> I have a very good native data set. However, the selenomethionyl
> crystal has a different space group and always suffers from
> radiation damage. A three-wavelength data set was still collected,
> and after phasing in SHARP, some features can be seen but the map is
> not good enough for tracing. Then I did some heavy atom soaking
> with the native crystals and collected data at home, however, the
> crystal was again converted into the same space group as the
> selenomethionyl crystal. At lease 4 Hg sites can be found both by
> isomorphous difference Fourier calculated using the partial Se-MAD
> phase and by isomorphous difference Patterson, suggesting they
> should be real. Now with these information, what's the best way to
> do the phasing in SHARP, or in some other programs?
>
> I hope I have made myself clear; and I would like to supply more
> details. Any suggestion will be highly appreciated.
>
> Best regards,
> Junyu
>
>
> ==============================
> Junyu Xiao
> Department of Biological Chemistry,
> University of Michigan
>
> Lab address:
> 3163 Life Sciences Institute
> University of Michigan
> 210 Washtenaw Avenue
> Ann Arbor, MI, 48109-2216
> Phone: 734-615-2078
> ==============================
>
>
>
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: pink/green paper?
From: James Murray James {- dot -} Murray {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-07-17

Next message:
Subject: Re: Advice for phasing
From: Jacob Keller j-keller2 {- at -} MD {- dot -} NORTHWESTERN {- dot -} EDU
Date: 2008-07-17