MR and pseudo-translationnal-symmetry

From: vincent Chaptal
Date: 13 March 2012 09:21

Dear ccp4,

I have a case of PTS and wonder what's the best strategy to handle my data.

I processed my data in C2 with a=161 b=109 c=225 beta=104. The data in 97% complete to 3,8A.
xtriage detected a 40% peak in the patterson at fractional coordinates x=-0,001 y=0,055 z=0,5.

I want to try to phase using MR.
Should I:
- leave the data in C2 (fully complete) and specify the program to use PST.
- expand from C2 to P1 and run using PST.
- re-index in P1 (a=98 b=97 c=225, alpha=78 beta=78, gamma=68) with only ca. 80% completeness, and specify PST.

before shooting more crystals to increase compleness and going for HA phasing, i was wondering if i could do something with what i have.
thank you for your input.
vincent

--
Vincent Chaptal, PhD

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From: Randy Read

Dear Vincent,

The easiest thing for you to do right now in the CCP4 context is to run Molrep, with the flag for PTS turned on.  If that works and gives a clear solution, that's great.  If not, then I'd suggest downloading a recent version of Phenix and trying the new version of Phaser that handles translational NCS, as in yesterday's discussion.

I don't think there's an advantage to reindexing, unless you have some reason to suspect that the true space group is not C2.  In some cases, if the translation is close enough to a lattice translation, you can assume an exact lattice translation and reindex in a smaller cell, throwing away the weak half of the data, but I think the y-component of your translation is too far from zero for that to be a reasonable alternative.

Best wishes,

Randy Read

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From: Garib N Murshudov

There are 3 options:

1) Use molrep. If you have two copies related with PST then it can give right solution

2) Take the latest version of phaser and use it. It can deal with PST with two related copies also

3) Reduce cell dimensions (it does not seem to be possible in your case. PST is not exactly on cell edges. But you can try). Work in c2 with smaller cell and then expand. 

but before going into all these trouble make sure that you really have PST. Calculating patterson (ccp4i, fft) and displaying using coot can give you some insight. Relation between origin and non-origin peaks can give you some insight. 

regards

Garib

Garib N Murshudov

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From: Eleanor Dodson
I would try molrep - it will detect the NC translation and use it..

Eleanor