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Hi,<br>
<br>
I would like to see this example too. <br>
<br>
You can define a bond between any pair of atoms, any number of
bonds, including bonds between symmetry related atoms. This is
explained in details here:<br>
<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles">http://phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles</a><br>
<br>
Example:<br>
<br>
refinement.geometry_restraints.edits {<br>
� bond {<br>
��� action = *add<br>
��� atom_selection_1 = chain A and resseq 123 and name O<br>
��� atom_selection_2 = chain Z and resseq 321 and name N<br>
��� symmetry_operation = -x-1/2,y-1/2,-z+1/2<br>
��� distance_ideal = 1.55<br>
��� sigma = 0.02<br>
� }<br>
}<br>
<br>
The best way to check that the bond you defined was actually used in
refinement is to find it in .geo file that lists all restrains used
in refinement.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 12/4/14 10:47 AM, Nigel Moriarty
wrote:<br>
</div>
<blockquote
cite="mid:CANkP=2eVA+wbZef9Sew9HZWN_Yf+cWPBUQtVHMtnjGkpsgbALg@mail.gmail.com"
type="cite">
<div dir="ltr">Jens
<div><br>
</div>
<div>You should try�</div>
<div><br>
</div>
<div>phenix.ligand_linking model.pdb</div>
<div><br>
</div>
<div>to see if that is helpful. I think, though, that you should
send me an example so I can check the best method.</div>
</div>
<div class="gmail_extra"><br clear="all">
<div>
<div class="gmail_signature">
<div dir="ltr">Cheers
<div><br>
</div>
<div>Nigel
<div><br>
</div>
<div>---</div>
<div>Nigel W. Moriarty<br>
Building 64R0246B, Physical Biosciences Division<br>
Lawrence Berkeley National Laboratory<br>
Berkeley, CA 94720-8235<br>
Phone : 510-486-5709� �� Email : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a><br>
Fax�� : 510-486-5909� � �� Web� : <a
moz-do-not-send="true" href="http://CCI.LBL.gov"
target="_blank">CCI.LBL.gov</a></div>
</div>
</div>
</div>
</div>
<br>
<div class="gmail_quote">On Thu, Dec 4, 2014 at 9:47 AM, jens j
birktoft <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:birktoft@nyu.edu" target="_blank">birktoft@nyu.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Everybody.
<div><br>
</div>
<div>Are there ways to restrain non-covalent interactions
between molecules in adjacent asymmetric units?</div>
<div>I know the custom bond procedure works well for
covalent bonds. However I also would like to add
restraints for (1) bond angles, (2) torsion angles (less
important) and (3) nucleotide base-pairing. I know that
all of these can be generated via the custom bond
syntax, but that is a rather tedious and time-consuming
process.� Perhaps there is a simpler way</div>
<div><br>
</div>
<div>I know this issue has been raised before but am
unaware of any new developments.</div>
<div><br>
</div>
<div>Cheers</div>
<span class="HOEnZb"><font color="#888888">
<div><br>
</div>
<div>Jens<br clear="all">
<div><br>
</div>
-- <br>
<div>
<div>+++++++++++++++++++++++++++++++++++++++++++++++++++<br>
Jens J.�<span
style="background-color:yellow;background-repeat:initial
initial">Birktoft</span></div>
<div><span
style="background-color:rgb(255,255,204);color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px">Director</span><span
style="color:rgb(136,136,136);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">�</span><span
style="background-color:rgb(255,255,204);color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px">of</span><span
style="color:rgb(136,136,136);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">�</span><span
style="background-color:rgb(255,255,204);color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px">Crystallography</span><span
style="color:rgb(136,136,136);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">�</span></div>
<div>Structural DNA Nanotechnology</div>
<div>Chemistry Department,<br
style="font-family:arial,sans-serif;background-color:rgb(255,255,255)">
New York University</div>
<div>e-mail:�<a moz-do-not-send="true"
href="mailto:jens.knold@gmail.com"
target="_blank"><span
style="background-color:yellow;background-repeat:initial
initial">jens</span>.<span
style="background-color:yellow;background-repeat:initial
initial">knold</span>@gmail.com</a>; Phone:
<a moz-do-not-send="true"
href="tel:212-749-5057" value="+12127495057"
target="_blank">212-749-5057</a><br>
very slow-mail: 350 Central Park West, Suite 9F,
New York, NY 10025<br>
+++++++++++++++++++++++++++++++++++++++++++++++++++</div>
</div>
</div>
</font></span></div>
<br>
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</blockquote>
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