That will work also.<br><br><div class="gmail_quote">On Wed, Feb 13, 2013 at 2:34 PM, Abhinav Kumar <span dir="ltr"><<a href="mailto:abhinavk@slac.stanford.edu" target="_blank">abhinavk@slac.stanford.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<div>How about using residue CME which is
the CYS and BME linked together.<br>
CME is included in the CCP4 monomer library, and so Phenix should
accept it without a dictionary file.<br>
<br>
<div><font face="Verdana" color="#000099">
Thanks, <br>
Abhinav </font>
<p><font face="Verdana" color="#000099">
</font>
<font face="Verdana" color="#0099AA">
JCSG@SSRL, SLAC <br>
<a href="tel:%28650%29%20926-2992" value="+16509262992" target="_blank">(650) 926-2992</a> <br>
</font></p>
</div><div><div class="h5">
On 02/13/2013 01:02 PM, Nigel Moriarty wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">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>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<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><br>
<br>
<br>
<br>
<br>
<br>
On 02/12/2013 11:21 PM, Rajeshwer Sankhala wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">
<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>
<br>
</div>
</div>
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-- <br>
Nigel W. Moriarty<br>
Building 64R0246B, Physical Biosciences Division<br>
Lawrence Berkeley National Laboratory<br>
Berkeley, CA 94720-8235<br>
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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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