Re: [ccp4bb]: big cell change, how to extend the phase?

[Edward Berry <eaberry@lbl.gov>]

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***



Jinsong Liu wrote:
> Recently I posted a question about solving patterson with translational
> symmetry.  Basically, the problem was solved by using one of the best
> quality data set. As I mentioned, every crystal showed big difference in
> the cell constant, so patterson for most of the crystal is almost
> impossible to solve. But finally I solved one of the dataset, now this
> Hg dataset only extend to 3.2A (process by scalepack, mosflm only
> process to 3.4A ), after SHARP SAD phasing, the FOM is around 0.4
> (accentric), 0.2 (centric). After SOLOMON, I can see the molecular
> boundary, and a few helixes.
> Now, I have another dataset by Br dipping, in house SAD data. Patterson
> is hard to solve again and anomalous signal may be weak. But it diffract
> to 2.5A. I want to extent the Hg SAD phase from 3.2A to this Br 2.5A.
> What is the best way to do it?
> These are the two cells:
> Hg: I222, 88x112x142
> Br: I222, 91x118x140
> 
If you feel the cells are too nonisomorphous to transfer the phases 
directly (which seems likely), and you can see the outline of your 
molecule, you could try molecular replacement using density as a 
search model. I think Eleanor Dodson outlined a procedure for this 
using CCP4 in the last year or so, that may be on the CCP4BB archive.
Also the amore documentation gives an example-
http://www.ccp4.ac.uk/dist/html/amore.html#example1b .

Since your density is quite poor you might use an unphased cross-rotation
function between the two crystals (almn and/or polarrfn) to limit the
rotation function solutions, which presumably should be a relatively 
small rotation since the cells are related. For the translation function 
you will depend on your density and amore or ttfc.

Then once you have low resolution MR phases for the second derivative
you may be able to locate some Br's by phased anomalous difference
maps and use them to obtain high-resolution phases and solve the
structure.  

A bit of multi-crystal averaging (DM-Multi) may help if the MR phases 
are not good enough to locate the Br's . Here the non-isomorphous
nature of your crystals is an advantage, as it means the molecular 
transform is sampled differently by the two crystals.

Ed