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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Pavel,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Sometimes truncation/mutation to poly-gly or poly-Ser is
desirable. If not already present could this be another option? Another
interesting option would be to be able to change OR keep the residue names of
the template to be mutated. Sometimes it is useful to chop the sidechains, but
still be able to tell what residue this is supposed to be via the residue name.
Again some of this may already be present, haven’t had a chance to play around
with this.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";
color:windowtext'>From:</span></b><span style='font-size:10.0pt;font-family:
"Tahoma","sans-serif";color:windowtext'> phenixbb-bounces@phenix-online.org
[mailto:phenixbb-bounces@phenix-online.org] <b>On Behalf Of </b>Pavel Afonine<br>
<b>Sent:</b> Wednesday, May 13, 2009 3:56 PM<br>
<b>To:</b> PHENIX user mailing list<br>
<b>Subject:</b> Re: [phenixbb] mutate to polyAla<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I just realized that you could do it even without using
truncate_to_polyala:<br>
<br>
phenix.pdbtools model.pdb keep="backbone"<br>
<br>
or, equivalently:<br>
<br>
phenix.pdbtools model.pdb remove="sidechain"<br>
<br>
and it works for both: proteins and RNA/DNA. <br>
<br>
Pavel.<br>
<br>
<br>
On 5/13/09 12:43 PM, Francis E Reyes wrote: <o:p></o:p></p>
<pre>Though the original question was for protein, is there a mutate to <o:p></o:p></pre><pre>poly C for RNA as well? :)<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>It just came to mind right now.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>FR<o:p></o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre>On May 13, 2009, at 1:42 PM, Pavel Afonine wrote:<o:p></o:p></pre><pre><o:p> </o:p></pre><pre> <o:p></o:p></pre>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><pre>Hi,<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>the next nightly build of PHENIX will have this option available from<o:p></o:p></pre><pre>phenix.pdbtools.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Example:<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>phenix.pdbtools model.pdb truncate_to_polyala=true<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>As always, any feedback will be very appreciated.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Pavel.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre>On 5/7/09 7:01 AM, Francis E Reyes wrote:<o:p></o:p></pre><pre> <o:p></o:p></pre>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><pre>Is there an option or a phenix.* utility to mutate a MR model to poly<o:p></o:p></pre><pre>ALA before the MR is done?<o:p></o:p></pre><pre><o:p> </o:p></pre><pre> <o:p></o:p></pre></blockquote>
<pre>_______________________________________________<o:p></o:p></pre><pre>phenixbb mailing list<o:p></o:p></pre><pre><a
href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><o:p></o:p></pre><pre><a
href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><o:p></o:p></pre><pre> <o:p></o:p></pre></blockquote>
<pre><o:p> </o:p></pre><pre>---------------------------------------------<o:p></o:p></pre><pre>Francis Reyes M.Sc.<o:p></o:p></pre><pre>215 UCB<o:p></o:p></pre><pre>University of Colorado at Boulder<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>_______________________________________________<o:p></o:p></pre><pre>phenixbb mailing list<o:p></o:p></pre><pre><a
href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><o:p></o:p></pre><pre><a
href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><o:p></o:p></pre><pre> <o:p></o:p></pre></div>
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