[ccp4bb] YATQ (yet another twinning question) - may involve pirates

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Shifting twin fraction with refinement - finally zero
From: Jon Schuermann schuerjp {- at -} ANL {- dot -} GOV
Date: 2010-04-23

Next message:
Subject: Re: YATQ (yet another twinning question) - may involve pirates
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-04-23

Subject: YATQ (yet another twinning question) - may involve pirates
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2010-04-23

In a nutshell
=============
Is there a way to make solve/resolve behave reasonably if the data
is twinned? Is there a recommended alternative path to clean up and
maybe even auto-trace a map with 4-fold NCS but twinned data?
Maybe Pirate/Buccaneer?

In detail
=========
I'm fighting with a structure that is probably/maybe in P4(2).

2.6A data 98% complete
Rmerge = 0.07 in P4
Rmerge = 0.16 in P422 (note the disturbingly low value)

Pointless is 88% confident it's P4(2).

Laue Group Lklhd NetZc Zc+ Zc- CC CC- Rmeas R-

= 1 P 4/m *** 0.916 4.68 9.36 4.67 0.94 0.47 0.09 0.30
10 P 4/m m m 0.000 6.83 6.83 0.00 0.68 0.00 0.20 0.00

Truncate says the data is twinned, with a twinning fraction of 0.25.
That is consistent with the bad-but-not-awful Rmerge in P422, right?

I have a promising initial MR solution in P4(2) with four monomers
in the a.s.u. It refines to R/Rfree = 0.36/0.38 in refmac but only if I
enable the twinned data option. Twinning fraction refines to
Twin fractions = 0.4322 0.5678

My thought was to use the 4-fold NCS and solvent flattening in resolve to
clean up and ideally auto-trace into the initial mediocre maps.
The resolution is not great, but the 4-fold NCS should help a lot.
Unfortunately, so far as I can figure out resolve ignores the twinning
and is stuck dealing with R > 0.60 and extremely poor maps.

I tried de-twinning the data, but this was not a great success.
Should I believe the truncate estimate of 25% twinning fraction
or the refmac estimate of 43%? Neither? In any case, feeding the
supposedly detwinned data to either refmac or resolve produces
worse results that I was getting before attempted detwinning.

Any advice?

--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Shifting twin fraction with refinement - finally zero
From: Jon Schuermann schuerjp {- at -} ANL {- dot -} GOV
Date: 2010-04-23

Next message:
Subject: Re: YATQ (yet another twinning question) - may involve pirates
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-04-23