Like Herman, it was not apparent to me what exactly you want wanted.
If you want a map that covers only [1] or excludes [2] a particular atom
selection then you can do that in Coot.
Extensions -> Maps... -> Mask Map by Atom Selection,
e.g. to show only the "A" chain, use an atom selection of "//A".
You can then export the map using:
Extensions -> Maps... -> Export Map
or
Extensions -> Maps... -> Export Local Map Fragment...
If you really want structure factors from that then you can use sfall
(MODE SFCALC MAPIN).
Paul.
[1] use mask inversion
[2] don't use mask inversion
------------------------------------------------------------------------
*From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On
Behalf Of *zhang yu
*Sent:* Sunday, February 19, 2012 11:47 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*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
