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Re: [ccp4bb]: NCS averaging

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Thanks for so many replies. I think I need to explain what I have done

Before this MAD  (2.2A) data set, we have a 2.4A native dataset and I have

tried MOLREP with a poor MR search model. The self rotation function did
show a proper two-fold.  After many trials in AMORE, MOLREP, all the
suggest that two molecules have the same rotation but with translation
shift by half
in Z (and less than 1/10 in y). This is in P21.  But the MR solutions is
not refinable.
so when I collected the MAD data, I tried GETAX after phased by SHARP, and
didn't work due to lack of proper 2-fold.
So that is why I want to find the better way to do NCS-averaging.
I will try use the MR solution to get a NCS mask and doube-check if the MR
is at least in the right place compared with the MAD map. And I will
consider so many
sugestions your guys offer and post a summary later.

Thanks again.


Clemens Vonrhein wrote:

> Dear Jinsong,
> if you have some kind of proper NCS (i.e. Cn or Dn symmetry) you could
> use a selfrotation function to determin the rotational part and GETAX
> to find the translation. There is an example script to do both in the
> CCP4 distribution:
>   $CCP4/examples/unix/non-runnable/getax-ncs-search
> Let me know if you need any help with this.
> Cheers
> Clemens
> > What is the easiest (or best) way to get a NCS matix out of a phased
> > map? I got below average MAD-phased map,  and I know
> > 2 Se position. There are 2 monomer per ASU.  I tried FINDNCS ( I also
> > have 4 very very weak Pt site positons), and the result seems not
> > very convincing.  From the non-averaged DM map, I can see the solvent
> > boundary, and I can barely see the two molecules.  I need to
> > get the correct NCS-mask, or correct NCS matrix. When I put the NCS
> > matrix I got from FINDNCS in DM, it didn't give me anything better
> > then I got non-averaged map.
> > I have also played with MAPROT, MAPMASK, NCSMASK, tried to get a ncs
> > mask but without success.
> > Thanks for any help.
> >
> > Jinsong
> >
> > PS: Anyone solved MAD with one Se in a 260 A.A. protein?  Any
> > experience? Thanks.
> >
> --
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"The DAO is not a real DAO when it can be talked about."
                                                ---(DAO DE JING)
Jinsong Liu, Ph.D.
Tularik Inc.
Two Corporate Drive                     Phone: 650 825-7054
South San Francisco, CA 94080, USA      Email: jsliu@tularik.com