Re: [ccp4bb] Finding NCS operator from one heavy atom site?

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

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Subject: Re: Finding NCS operator from one heavy atom site?
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2008-05-22

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Subject: Re: Finding NCS operator from one heavy atom site? (long)
From: Phil Jeffrey pjeffrey {- at -} PRINCETON {- dot -} EDU
Date: 2008-05-22

Subject: Re: Finding NCS operator from one heavy atom site?
From: Jan Abendroth jan {- dot -} abendroth {- at -} GMAIL {- dot -} COM
Date: 2008-05-22

Hi Partha,
ncs6d did really great things to me a while ago. Similar case as yours, only
one Met site in each of the 4 monomers, pretty horrible maps. I was amazed
how ncs6d could sort its way through the maps and find the ncs operators. As
a simple approach I just took a spherical map around the methionine site.
In fact it seemed to be easier to find the ncs between two dimers first,
improve the operators with imp and then search for the missing operators
within the dimer.
Sorry, don't have any clever scripts for that, did it all by hand.

The maps improve a lot after averaging. However, almost needles to say that
cloning, expressing, purifying, crystallizing and solving the same construct
of an 85% seq. identical ortholog took less effort than messing around with
the bad maps...

Good luck
Jan

2008/5/22 Partha Chakrabarti :

> Hi,
>
> Apologies for a non CCP4 question in strict sense. I am trying to work
> out the NCS operators for a three wavelength
> Se-MAD data which has only one site. The map is hardly interpretable.
> I came across the USF Rave package and what I am aiming is
>
> creak a mask around the heavy atom site (found by SHELX or Solve)
> using mama or so, (ideally from resolve.mtz but not necessarily),
>
> translate it to the other heavy atom site(s),
> give a 6d search with NCS6d and
> perhaps refine the best CC a bit with imp.
>
> If it works, I could try use the NCS operator in DM or Resolve etc.
>
> I was wondering if someone has a C-shell scripts for dealing with such
> situation already. Of course if there are other programs for such a
> task within CCP4, could give it a try.
>
> Best Regards,
> Partha
>

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

Previous message:
Subject: Re: Finding NCS operator from one heavy atom site?
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2008-05-22

Next message:
Subject: Re: Finding NCS operator from one heavy atom site? (long)
From: Phil Jeffrey pjeffrey {- at -} PRINCETON {- dot -} EDU
Date: 2008-05-22