<html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"></head><body >Excellent point. The difference between using bme and cme is rather ideological. I would say that incorporating cme implies that your protein was somehow synthesized with non-canonical amino acid. Usind bme seems more in line with what actually happens - betamercaptoethanol forming disulfide bond with a cysteine.<div><br></div><div>In practical sense, both things work. Until IUCr comes up with a convention, one is free to ignore ideological considerations :)</div><div><br></div><br><br><br>-------- Original message --------<br>From: Abhinav Kumar <abhinavk@slac.stanford.edu> <br>Date: <br>To: phenixbb@phenix-online.org <br>Subject: Re: [phenixbb] how to make covelent link of BME with Cys and refine <br> <br><br>
<div class="moz-cite-prefix">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 class="moz-signature"><font size="2" face="Verdana" color="#000099">
Thanks, <br>
Abhinav </font>
<p><font size="2" face="Verdana" color="#000099">
</font>
<font size="2" face="Verdana" color="#0099AA">
JCSG@SSRL, SLAC <br>
(650) 926-2992 <br>
</font></p>
</div>
On 02/13/2013 01:02 PM, Nigel Moriarty wrote:<br>
</div>
<blockquote cite="mid:CANkP=2cc3V95C_ZVDA5UbCqNmh=UewUnmySoNzZ+O1nDHpzpZw@mail.gmail.com" 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 moz-do-not-send="true" 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 class="h5"><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 class="h5">
<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>
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