Peter
Yes, by "2Fo-Fc type maps " I was including the weighted maps you
mention (which should be better).
The main issue is whether 3mF(obs)-2DF(calc) and higher coefficients
would be better for the twinned reflections
Regards
Colin
________________________________
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On
Behalf Of Peter Chan
Sent: 29 October 2010 18:59
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Help with model bias in merihedral twin +
Refmac5
Dear Colin,
Thank you for the email. To be honest, I don't know exactly
which map they are. From my understanding (and according to
http://www.ccp4.ac.uk/schools/India-2010/tutorials/refmac/Murshudov30th.
pdf), Refmac5 outputs 'normal map' 2mF(obs)-DF(calc) and 'difference
map' 2mF(obs)-DF(calc). I believe this is better than looking at the
typical 2F(obs)-F(calc), although there still appears to be a fair
amount of model bias.
Best,
Peter
________________________________
Subject: RE: [ccp4bb] Help with model bias in merihedral twin
Date: Wed, 27 Oct 2010 17:38:41 +0100
From: colin.n...@diamond.ac.uk
To: pc...@hotmail.com
Peter
Regarding the question
"Although the electron density map looks good, I am not sure if
I should have too much confidence in it because I was not able to obtain
'strong electron densities' from omitted sections of the model in a
refinement. I don't know if this is an indicator for bias introduced
somewhere. I would like to ask what may be some procedures I can try for
checking and removing these biases"
Can you state what type of maps these are?
The reason is the following. Taking PHENIX twinning maps as an
example we have, in the manual -
"By default, data is detwinned using algebraic techniques,
unless the twin fraction is above 45%, in which case detwinning is
performed using proportionality of twin related Icalc values. Detwinning
using the proportionality option, results in maps that are more biased
towards the model, resulting in seemingly cleaner, but in the end less
informative maps. The 2mFo-dFc map coefficients can be chosen to have
sigmaA weighting (two_m_dtfo_d_fc) or not (two_dtfo_fc). IN both cases,
the map coefficients correspond to the 'untwinned' data. A difference
map can be constructed using either sigmaA weighted detwinned data
(m_dtfo_d_fc), a sigmaA weighted gradient map (m_gradient) or a plain
gradient map (gradient). The default is m_dtfo_d_fc but can be changed
to gradient or m_gradient if desired. "
For the high twin fraction which you have (near 50%). my view is
that 2Fo-Fc type maps are not optimal for this as they don't take
account of the increased bias resulting from the extra degrees of
freedom (i.e. splitting the intensity between the two reflections based
on Icalc). For the reflections related by twinning higher order
coefficients (e.g. 3Fo-2Fc or perhaps 4Fo-3Fc) would give noiser but
less biased maps.
Fibre diffraction folk do similar things when their Bessel
function terms overlap.
Cheers
Colin
________________________________
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk]
On Behalf Of Peter Chan
Sent: 27 October 2010 02:00
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Help with model bias in merihedral
twin
Hello All,
Not long ago I posted for some help with my twinned
dataset at 1.95 A, and have confirmed the twinning of P6(5) into
P6(5)22. Molecular replacement was successful and the twin refinement in
Refmac yieled R/Rfree of 21%/26%, with a twin fraction of 0.46.
Although the electron density map looks good, I am not
sure if I should have too much confidence in it because I was not able
to obtain 'strong electron densities' from omitted sections of the model
in a refinement. I don't know if this is an indicator for bias
introduced somewhere.
I would like to ask what may be some procedures I can
try for checking and removing these biases, and a few additional related
questions.
As suggested to me previously, I have generated a total
omit map with sfcheck in ccp4i, using the refined pdb and unrefined data
in P6(5). The .map file look a little worse in quality (is this because
of the twinning?) but is still reasonable, with a few breaks in the main
chain and side chains. Interestingly, when I do a real space refinement
against the total omit map, I get slightly better Rfree at the earlier
rounds of Refmac which diverges into the numbers above. Why is this the
case?
Cycle R fact R free
0 0.2301 0.2523
1 0.2205 0.2534
2 0.2164 0.2545
3 0.2140 0.2554
4 0.2123 0.2559
5 0.2117 0.2570
6 0.2116 0.2575
7 0.2112 0.2582
8 0.2112 0.2584
9 0.2109 0.2587
10 0.2106 0.2597
Secondly, I read that I should make sure the Free R
flags should be consistent throughout the twin-related indices. What may
be the adverse outcome if this isn't enforced? Is Refmac aware of this
in a twin-refinement? If not, which tool could I use for this?
I would very much appreciate any comments and
suggestions.
Best,
Peter Chan
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