Re: [ccp4bb] How to subtract one electron density map from another

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

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From: "David J {- dot -} Schuller" djs63 {- at -} CORNELL {- dot -} EDU
Date: 2007-03-22

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Subject: Re: How to subtract one electron density map from another
From: "Edward A {- dot -} Berry" EABerry {- at -} LBL {- dot -} GOV
Date: 2007-03-22

Mapman (Uppsala software factory) allows you to subtract maps
if they are on the same grid. You may need to multiply one
map by a factor (again in mapman) to make the background flat
in the regions you believe to be identical.

Linearity of the Fourier Transform implies you could get
the same result by subtracting in reciprocal space.
However if the crystals are not perfectly isomorphous,
it may help to "skew" one map onto the others before
subtracting, i.e. apply a rotation-translation operator
to superimpose equivalent areas, which could be a reason
for doing it in real space.

You can do this with
"mave" (also USF), getting the operator by superimposing
models in O or lsqman, or, if the refinement has not
progressed that far, refining the operator from identity
with the "improve" option of mave.

I expect mapmask and friends of dmmulti can do all this too,
but I am less familiar with the CCP4 tools. Either way,
there is certain amount of documentation you will need
to read in order to "know how to use it". But that is
time well spent in the long run, as it will help you to
interpret the results or modify the procedure as new
situations arise. If you get stuck and have specific
questions, the BB is hear to help!

Ed

CCP4bb navigation

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

Previous message:
Subject: Re: X-ray generator uninterruptible power supply
From: "David J {- dot -} Schuller" djs63 {- at -} CORNELL {- dot -} EDU
Date: 2007-03-22

Next message:
Subject: Re: Highest shell standards
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-23