<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi, <br>
<br>
or alternatively:<br>
<br>
phenix.map_box model.pdb map_coefficients.mtz selection="chain A"<br>
<br>
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.<br>
<br>
Pavel<br>
<br>
On 2/19/12 3:46 PM, Terwilliger, Thomas C wrote:
<blockquote
cite="mid:AD56E2411D1DF44889DF34878BB3307906796460@ECS-EXG-P-MB01.win.lanl.gov"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<style type="text/css" id="owaParaStyle"></style>
<div style="direction: ltr;font-family: Tahoma;color:
#000000;font-size: 10pt;">Hi Yu Zhang,
<div><br>
</div>
<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>
<div><br>
</div>
<div>All the best,</div>
<div>Tom T</div>
<div><br>
<div style="font-family: Times New Roman; color: #000000;
font-size: 16px">
<hr tabindex="-1">
<div id="divRpF758319" style="direction: ltr; "><font
color="#000000" face="Tahoma" size="2"><b>From:</b>
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>
[<a class="moz-txt-link-abbreviated" href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>] on behalf of Zhang
yu [<a class="moz-txt-link-abbreviated" href="mailto:phenixzyfish@gmail.com">phenixzyfish@gmail.com</a>]<br>
<b>Sent:</b> Sunday, February 19, 2012 4:42 PM<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> [phenixbb] FFT map coefficients only for
certain chains<br>
</font><br>
</div>
<div>Dear Phenixers,<br>
<br>
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.
<br>
<br>
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>
<br>
Thanks.<br>
<br>
Yu Zhang<br>
</div>
</div>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<br>
</body>
</html>