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Hmm - You say you have the Se positions in the P3121 form, plus some roughly placed helices, so you should be able to get the matrices which interconvert the three P3121 molecules. (there are superpose coordinate programs. GESANt or LSQKAB, which will give these..)

and PHASER output gives you the rotation angles and translation vector to take stuff from P3121 form to I222

(By the way is there any sign of se positions in the I222 form?)

You can use

PDBSET xyzin P3121-bits.pdb xyzout I222-shiftedbits.pdb with keywords like this - BUT CHECK!!

ROTAT EULER alpha beta gamma - set 1

SHIFT frac Tx Ty Tz ( prob got that wrong but check documentation to move those coords)

CELL A I222 B_I222 etc

SYMM I222

End

And repeat for set 2

Then look at the DMMULTI documentation -

You can average over the three P3121 copies and the two I222 copies with appropriate rotation matrices

There are many ways to get the matrices wrong! but transforming the trial cds in the right order should work..

On Wed, 9 Jan 2019 at 16:43, <[log in to unmask]> wrote:

Dear Andy,

Best would be to convert the phaser angles (plus vector) in a matrix (plus vector) and use this for your transformations. The phaser people should be able to provide you with information how to do this, since they have to do it in order to produce their output files. Alternatively, you may try to find a transformation program which takes phaser angles as an input. I do have some prehistoric subroutines which do all kind of conversions between angles and matrices, and if nothing works, I could have a look if one of those subroutines could to the job.

Best,

Herman

Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Andrew Lovering
Gesendet: Mittwoch, 9. Januar 2019 17:08
An: [log in to unmask]
Betreff: [EXTERNAL] [ccp4bb] complex multi-crystal averaging

Dear All,

I suspect the way out of this is a new crystal (!) but interested to hear any advice.

I have two crystal forms of a 500aa protein, vaguely tube-shaped

1=P3121, diffracts to 4.1 ang, 3 copies in asu, 86% solvent; map indicates it is a relative of other folds (but those are not so close that they’d be a good guide to sequence register). I have selenomet SAD phases which helps identify Met positions. The 3-fold and high solvent give a great map but you wouldn’t want to build it and buccanner and phenix think similar

2=I222, 2 copies per asu, 66% solvent. This has a cell that gives wildly anisotropic diffraction – ~3, 3.5, 4.3 down different axes. Not really rectified by staraniso. No phases

So I can cut the density out of form 1 map (using secondary structure elements of a rough PDB as a mask), and use phaser with this density as search model to find the two copies with a TFZ of about 10. The phaser map shows a bit of detail and the solution has placed the protomers such that they agree with a self-rotation function. Phenix find_ncs on phaser map similarly agrees (as I would expect).

Now...I have an eye on multi-crystal averaging between the two forms. BUT the phaser map isn’t good enough to manually place the PDB used in cut-out density, and I can’t see a straightforward way of using the angle info in phaser sol to perform a co-ordinate transformation (but I think ccp4bb users will put me right on this – I’d imagine placing the PDB into the cutout density mtz then using PDBset?). I tried converting the phaser mtz to a map using FFT then using phased TF in Molrep to place the PDB but this didn’t work, complaining about the grid used.

One last caveat – I have multiple sets for the I222 that intriguingly differ by 12 angstrom down a 240 ang axis: doing multi-crystal averaging between these two forms achieves little when I would expect otherwise (all the NCS correlations are good, high initial agreement)

Like I said...fingers crossed for a new crystal form!

Andy

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