Dear Yu,
You seem to be mixing up map coefficients and map files. Map coefficients are
modified reflections, e.g. 2*Fobs-Fcalc multiplied by a weighting factor with
h,k,l indices and are stored in a .mtz file. From these map coefficients, you
can calculate a map file with an FFT program. A map is an array with local
values of the electron density spaced say 1Å apart with extentions like .map.
If you provide Coot with just map coefficients, it will calculate on the fly
the map around your centering atom so it does not need a map file.
Since every part of real space (the contents of the unit cell) contributes to
every reflection, it is not possible to generate "observed" map coefficients
for one chain alone. I do not know what options you exactly tried, but
normally, if you select a certain chain, it will calculate a map based on all
chains, but only output the map around the selected chain.
To get map (coefficients) of only one chain, there are two options:
1) a straight Fcalc map. Only input a pdb file with the chain you want to
select. Do not use observed F's. You will get calculated density for that chain
only and the rest of the map will be empty (zeroes).
2) a (vector difference) Fo-Fc omit map. Input a pdb file without the chain you
want to select and calculate an Fo-Fc map. All chains will be subtracted from
Fo with the exception of the chain you left out from the Fc calculation. This
map will contain density of the omitted chain plus noise due to the fact that
your model is imperfect (the famous 20% Rfactor of well-refined structures).
The generate a vector difference map, you should use phases calculated for the
complete model for Fo, and omit-phases for Fc.
I hope this clarified things a bit,
Herman
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of
zhang yu
Sent: Sunday, February 19, 2012 11:47 PM
To: [email protected]
Subject: [ccp4bb] FFT map coefficients only for certain chains
Dear CCP4ers,
Is that possible to generate map coefficients only for certain chains?
For example, I have two chains, A and B, and I would like to output a map file
only contains coefficients for chain A. The "isomesh" command in Pymol could
generate similar images. But my purpose is not for presentation, I need a map
file only contains coefficient for certain chains.
In the interface of "FFT" tool in Phenix or CCP4, there is an option to
include a PDB file and define atom selections. It describe that "If a PDB is
supplied, the output map will cover the model plus a buffer on all sides. The
atom selection parameters can be used to specify a smaller region" . If I
define the selection as chain A when I run the FFT, the output map still covers
a rectangular block containing chain A, instead of regions only surrounding
chain A.
Thanks.
Yu
--
Yu Zhang
HHMI associate
Waksman Institute, Rutgers University
190 Frelinghuysen Rd.
Piscataway, NJ, 08904
