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Hi <span style="font-size:14px">Xiang,<br>
<br>
Oleg's email says "</span><span style="font-size:14px">I'd
recommend dev-2006 nightly build". So please use that version of
Phenix and it should work. If it doesn't please get back to us and
we will do our best to make it work. Again, it will not work in "</span><span
style="font-size:14px"><span style="font-size:14px">PHENIX-1.9-1692</span>".<br>
<br>
All the best,<br>
Pavel<br>
</span><br>
<div class="moz-cite-prefix">On 4/22/15 11:19 AM, 李翔 wrote:<br>
</div>
<blockquote
cite="mid:CAE5L1v9+zPhaW-Y=Smb1pmC4ukQKND8G30KSUhp5OOSYQgHX8A@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Oleg,
<div><br>
</div>
<div>Thanks for the email. I tried to add "<span
style="font-size:14px">option secondary_structure.enabled=</span><span
style="font-size:14px">True</span>" in the <span
style="font-size:14px">geometry minimization but it does not
work. I also tried to prepare the restraint file with the
same command your provide above. However, on my computer it
says cif file is required and it does not recognize the
generated restraint</span><span style="font-size:14px"> file.</span></div>
<div><span style="font-size:14px"><br>
</span></div>
<div><span style="font-size:14px">Maybe there is something wrong
with my laptop or setting and I will also try the newest
version of PHENIX. Currently I am using PHENIX-1.9-1692.</span></div>
<div><span style="font-size:14px"><br>
</span></div>
<div><span style="font-size:14px">Thanks for your kind help!</span></div>
<div><br>
</div>
<div><span style="font-size:14px">Sincerely,</span></div>
<div><span style="font-size:14px">Xiang</span></div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">2015-04-22 12:20 GMT-04:00 Oleg Sobolev
<span dir="ltr"><<a moz-do-not-send="true"
href="mailto:osobolev@lbl.gov" target="_blank">osobolev@lbl.gov</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Dear Xiang,
<div><br>
</div>
<div>The simplest way to restrain basepairs in DNA would
be option secondary_structure.enabled=True. If this
doesn't work for you in the way you are expecting, try
to generate basepairs to restrain by using
phenix.secondary_structure_restraints
<your_model.pdb>. This will output restraints in
form of phil file. You may inspect it to make sure
basepairs are correct. Then you can supply this file to
geometry minimization along with
secondary_structure.enabled=True
secondary_structure.find_automatically=False options.
This should do the work. You will need relatively fresh
version of Phenix, I'd recommend dev-2006 nightly build.</div>
<div><br>
</div>
<div>This is relatively new feature, so feel free to
provide feedback and get back to us if something doesn't
work as you expecting.</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Oleg Sobolev.</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">
<div>
<div class="h5">On Wed, Apr 22, 2015 at 8:34 AM, 李翔 <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:lixiang1642@gmail.com"
target="_blank">lixiang1642@gmail.com</a>></span>
wrote:<br>
</div>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div class="h5">
<div dir="ltr">Hi everyone,
<div><br>
</div>
<div>I am trying to build some DNA duplex models
with different pitches by 3DNA. After changing
the pitches from the original duplex model, I
refined the duplex in PHENIX with geometry
minimization. However, the basepairing get
completely distorted. </div>
<div><br>
</div>
<div>Is there a quick way to generate the cif
file for basepairing in PHENIX or are there
any other better ways to keep the basepairing
restraint during the model refinement? </div>
<div><br>
</div>
<div>Thank you very much for your kind help!</div>
<div><br>
</div>
<div>Sincerely,</div>
<div>Xiang <span><font color="#888888"><br
clear="all">
<div><br>
</div>
-- <br>
<div>Li Xiang <br>
Department of chemistry,<br>
University of Michigan<br>
Email：<a moz-do-not-send="true"
href="mailto:lixiang1642@gmail.com"
target="_blank">lixiang1642@gmail.com</a></div>
</font></span></div>
</div>
<br>
</div>
</div>
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-- <br>
<div class="gmail_signature">Li Xiang <br>
Department of chemistry,<br>
Purdue University<br>
Email：<a moz-do-not-send="true"
href="mailto:lixiang1642@gmail.com" target="_blank">lixiang1642@gmail.com</a></div>
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