Herman, Thanks for clarifying the difference between map coefficients and map files for me. What I really need are only map files, and I could generate those masked maps by following Paul's suggestion.
Yu 2012/2/20 Paul Emsley <[email protected]> > > 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:[email protected]<[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 > > > > -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
