Raj<div><br></div><div>In the more recent versions of PHENIX, phenix.refine can found and link atoms closer than 3 angstrom if you specify intra_chain=True. In the older versions, you can use phenix.ligand_linking to generate the needed files.</div>
<div><br></div><div>Nigel</div><div><br></div><div>PS PHENIX does not read SSBOND or LINK records but there is a script to generate the link files from the LINK records.<br><br><div class="gmail_quote">On Tue, Feb 12, 2013 at 11:56 PM, Sabine Schneider <span dir="ltr"><<a href="mailto:sabine.schneider@mytum.de" target="_blank">sabine.schneider@mytum.de</a>></span> wrote:<br>
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<div>Hello Raj,<br>
<br>
do you have the link specified in you PDB file?<br>
Here is an example for an disulphide bond. Usually the link is the
line above the CRYST1 card.<br>
<br>
SSBOND�� 1 CYS A� 123��� CYS A� 123�������������������������
1555�� 8555� 2.12� <br>
<br>
Best,<br>
Sabine<div><div class="h5"><br>
<br>
<br>
<br>
<br>
<br>
On 02/12/2013 11:21 PM, Rajeshwer Sankhala wrote:<br>
</div></div></div>
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<p>Hello,</p>
<p>I can see additional density just next to Cys residues in my
protein structure and it looks like BME is covalently linked
to cys. I could form a disulfide bond between BME and Cys in
"Refmac 5 review restrain" but when i subject it for
refinement BME is thrown away (no disulfide bond). I also
given Cif file in refinement but it didnot help. I have a feel
that i am missing something in cif file. Can anyone suggest
step� by step starting from adding BME to making a link with
BME (Cys-BME)�and then refinement?</p>
<p>�</p>
<p>Raj</p>
</div>
<br>
<fieldset></fieldset>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>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 : NWMoriarty@LBL.gov<br>
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