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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Yu Zhang,
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<div>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!</div>
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<div>All the best,</div>
<div>Tom T</div>
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<div id="divRpF758319" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><b>From:</b> phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Zhang yu [phenixzyfish@gmail.com]<br>
<b>Sent:</b> Sunday, February 19, 2012 4:42 PM<br>
<b>To:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> [phenixbb] FFT map coefficients only for certain chains<br>
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<div>Dear Phenixers,<br>
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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.
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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.<br>
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Thanks.<br>
<br>
Yu Zhang<br>
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