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Hi John,<br>
<br>
what you have found in FAQ is for the command line version of
phenix.refine.<br>
<br>
In the GUI you most likely see something like <br>
<br>
"""<br>
Anomalous scatterer group (1)<br>
<br>
Atom selection :<br>
"""<br>
<br>
So you need to type atom selection string in "Atom selection : "
prompt. It should select your CD atoms. Something like this<br>
<br>
element Cd<br>
<br>
or<br>
<br>
chain X and resname LIG and name CD<br>
<br>
For more examples of atom selection syntax see phenix.refine manual
section "Atom selection examples":<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/documentation/refinement.htm">http://www.phenix-online.org/documentation/refinement.htm</a><br>
<br>
Let me know if you have any questions or problems. Also, you can
send me a PDB file and I will reply back with the directions on how
you should select your Cd atoms.<br>
<br>
Pavel.<br>
<br>
<br>
<br>
On 8/26/10 9:41 PM, John Rose wrote:
<blockquote
cite="mid:3E3AED3F-9535-4659-A67F-8CD97FB33DF2@bcl4.bmb.uga.edu"
type="cite">Hi,
<div><br>
</div>
<div>I am refining my first structure (Cd-SAD) with the Phenix
(GUI) and would like to refine anomalous f' and f". When i
check the box, a menu appears and I have no idea of how to
define the Cd atoms.</div>
<div><br>
</div>
<div>I looked at the help and FAQ and found this:</div>
<div><span class="Apple-style-span" style="font-family: monospace;
font-size: 14px; white-space: pre;">refinement.refine.anomalous_scatterers
{</span></div>
<span class="Apple-style-span" style="font-family:
verdana,helvetica,arial,sans-serif; font-size: 14px;">
<pre class="literal-block"> group {
selection = name BR
f_prime = 0
f_double_prime = 0
refine = *f_prime *f_double_prime
</pre>
</span>
<div>So I thought the name should be input as CD in the gui but
when I submitted the refinement I got an error.</div>
<div><br>
</div>
<div>Any help here would be appreciated? </div>
<div><br>
</div>
<div>Thanks,</div>
<div><br>
</div>
<div>John Rose</div>
<pre wrap="">
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