On Fri, May 20, 2011 at 2:42 PM, Krystle Williams McLaughlin <span dir="ltr">&lt;<a href="mailto:krystle_w@hotmail.com">krystle_w@hotmail.com</a>&gt;</span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">





<div>I have already run a BRU molecule through ReadySet and when I use the cif file generated from this phenix.refine will run through but when the Bromine atom is in the structure has a large negative density peak in the Fo-Fc map.</div>

</blockquote><div><br></div><div>This could just be radiation damage - assuming the Br is in the correct position as judged by the 2Fo-Fc map, it doesn&#39;t have anything to do with the restraints used.  I don&#39;t know if there&#39;s a reference for this, but I was told that brominated nucleotides are extremely sensitive to radiation damage, much worse than SeMet.  Did you use this for phasing?</div>

<div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div> I think it may just be a naming thing. BRU is already in the monomer library so I don&#39;t understand why I get an error at first also without the readyset cif file.</div>

</blockquote><div><br></div><div>It isn&#39;t in the version of the monomer library we distribute - many of the files in the full version are incomplete, and we don&#39;t include those.  ReadySet does have access to the Chemical Components Database definition of BRU, however, which it probably used to make the restraints.</div>

<div><br></div><div>-Nat</div></div>