Hi,
How about this:
1. Expand solution A to fill an unit cell
2. Expand solution B to fill 3 x 3 x 3 = 27 unit cells
3. Superpose 1 to 2 en bloc
Now we have a common origin,
because components of the origin shift vector is within -1 to 1.
4. Delete everything outside the ASU
5. Match chains if necessary
Best regards,
Takanori Nakane
On 2014-09-11 12:56, Seijo, Jose A. Cuesta wrote:
> Correction: that won’t fix any origin issues, only cell and
> assymetric unit.
>
> ================================
>
> Jose Antonio Cuesta-Seijo, PhD
>
> Carlsberg Laboratory
>
> Gamle Carlsberg Vej 10
>
> DK-1799 Copenhagen V
>
> Denmark
>
> Tlf +45 3327 5332
>
> Email [log in to unmask]
>
> ================================
>
> FROM: CCP4 bulletin board [mailto:[log in to unmask]] ON BEHALF OF
> Eleanor Dodson
> SENT: Thursday, September 11, 2014 11:44 AM
> TO: [log in to unmask]
> SUBJECT: [ccp4bb] making sure related molecules occupy the same space
>
>
> Here is a very common scenario for me.
>
> You run several MR jobs, say to search for 2 mols/asymm unit , maybe
> with different models or using different programs..
>
> You get several solutions, probably on different origins and/or
> related by some symmetry operator.
>
> How best to overlap them?
>
> My way is this:
>
> Use PISA to assemble all solutions from each run into a compact
> molecule (It does this by applying allowed symmetry operators.)
>
> Calculate SFS from each solution, combine them and use PHASEMATCH to
> find the origin shift .
>
> Move solution two to the same origin as solution one.
>
> Now check for fitting - remembering that if both solutions have chains
> A B there is no guarantee that A2 maps to A1 and B2 to B1.
>
> So I superpose A2 onto A1, A2 onto B1 etc till I find a transformation
> matrix that is indeed a symmetry operator..
>
> (You can do this in coot providing you can find the output matrix on
> the screen!)
>
> Then apply that symmetry to move A2 B2 to overlap A1 B1 ( or maybe B1
> A1) as appropriate..
>
> Obviously this is a pain in the neck!
>
> Does anyone have a neater solution??
>
> eleanor
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