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CCP4BB  September 2009

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Subject:

Summary for "Anisotropic Diffraction In Refinement" question

From:

Justin Hall <[log in to unmask]>

Reply-To:

Justin Hall <[log in to unmask]>

Date:

Tue, 15 Sep 2009 13:48:15 -0700

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (60 lines)

Dear All;

In response to my "Anisotropic Diffraction In Refinement", which asked  
for suggestions for how best to proceed with refinement with an  
anisotropic data set, I received a large number of responses which  
overwhelmingly suggested using the UCLA Anisotropy Server  
(<http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/>).

The Anisotripy Server treats scaled/truncated data sets (I used Scala  
and the old Truncate program). Fo and SigFo are analyzed with respect  
to resolution in three dimensions and the data treated in three steps:
1) An elliptical resolution boundary is determined and applied.
2) A purely anisotropic B-factor is applied to the Fo and SigFo data  
to cause the data in all directions to fall off equally.
3) A negative isotropic B-factor is then applied to the structure  
factors to force the fall-off in the strongest direction to match that  
of the original data, effectively meaning that the data are not scaled  
to the mean but the weaker data are scaled up to match the strongest  
data.

Application of a elliptical resolution boundary is justified because  
the resolution boundary from common integration programs (Denzo and  
Mosflm for example) is spherical where diffraction for anisotropic  
data is ellipsoidal. A spherical boundary would result in the  
inclusion of numerous poorly measured reflections in the higher  
resolution shells which effectively makes these data more noisy.  
Imposing an ellipsoidal resolution boundary is equivalent to removing  
noise from the higher resolution bins and is simply the anisotropic  
equivalent of the normal resolution limit truncation.

However, I was confused by the second and third steps.  The second  
step of application of anisotropic scale factors is appropriate if the  
refinement program does not include anisotropic scaling in its  
calculation of Fc, however modern refinement programs do this. Pavel  
Afonine touched on this in his CCP4BB general posting in response to  
my original posting where he noted that "anisotropic scale factor[s]  
that [are] part of the total structure factor take care of this"  
(<https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0909&L=CCP4BB&T=0&F=&S=&P=8362>).

For the third step, applying a negative isotropic B-factor to modify  
the Fo is equivalent to sharpening the peaks in your maps and this can  
be useful.  However, applying the correction to Fo will also result in  
an inappropriate decrease in the average temperature factor of the  
resulting model.  Since B-factors are used as a measure of the  
coordinate error of an atom, modifying your Fo means these low B  
factors will tend to confuse the users of that model
into thinking its quality is better than it really is. If a sharper  
map makes identification of model errors easier, the map can be  
sharpened when it is calculated, without affecting the parameters in  
the PDB file.  The latest versions of Coot, for example, allows you to  
sharpen any map that it calculates.

I brought these points to the attention of the Anisotropy Server  
director (Michael Sawaya), who is now working to provide an option to  
omit steps 2 and 3 for users who do not what their structure factors  
modified.

My thanks to everyone who responded to my original question, and to  
Dale Tronrud and Michael Sawaya in particular for valuable discussion.

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