[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[ccp4bb]: Data Sharpening Summary

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

Hi everyone-

I recently inquired about applying a negative B-factor to Fobs to
achieve a sharpening effect on the structure factors.  This has been
used to improve electron density maps and refinement/averaging in the
past by many people, including (in addition to those mentioned in my
original post) the potassium channel structure from Rod Mackinnon's

Thanks to all who replied, here is a brief summary:

David Borhani wrote with advice based on his experience with
Apolipoprotein AI.  They wrote a modified version of truncate that would
apply the artificial B-factor to the data, but this was never
incorporated into the general release of CCP4.  He had good suggestions
on low resolution refinement as well.

Rod Mackinnon used Xplor to calculate an anisotropic B-factor array,
applied this to the F's and converted his Sigmas manually by using
Sigmanew=(Fnew/Fold)sigmaold.  This is equivalent to directly applying
the scalar calculated from exp(-Bsin**2theta/lambda**2) to the F's and
Sigmas.  This was also pointed out by EJD, of course I should have
realized that this is the case!

David Schuller suggested Ecalc,  but I didn't want to normalize the F's
at the same time.

Fred Vellieux suggested using the BIOMOL suite of programs, which we
don't have installed here.

I subsequently figured out that you can use SFTOOLS to apply functions
(real or complex) to various columns of data, but didn't get around to
using it yet because:

Eleanor Dodson saves the day with a modified version of CAD that will
apply an overall B and Scale factor to the data.  This version should be
available publicly soon (if not already).  Check the Daresbury site if

Thanks again to everyone for their ideas and to EJD for the new version
of CAD!