Hi Yu Zhang, You can use the tool "phenix.cut_out_density" to select density from a map within a radius you define of atoms in a PDB file that you supply. I hope that helps! All the best, Tom T ________________________________ From: [email protected] [[email protected]] on behalf of Zhang yu [[email protected]] Sent: Sunday, February 19, 2012 4:42 PM To: [email protected] Subject: [phenixbb] FFT map coefficients only for certain chains Dear Phenixers, 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 Zhang