Hi,

or alternatively:

phenix.map_box model.pdb map_coefficients.mtz selection="chain A"

will create a box with map and model in it. The output will be a pdb file with the chain A, and a map in a box around chain A output in three different formats: X-plor, MTZ file with map coefficients and CCP4 map.

Pavel

On 2/19/12 3:46 PM, Terwilliger, Thomas C wrote:

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
_______________________________________________
phenixbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/phenixbb