<div dir="ltr">Miyatake<div><br></div><div>The OXT atom in the restraints file is there because it can be in the model. You need to remove the atom from the model if you don't want it.</div><div><br></div><div>Also, Coot's make link does not make a link in Phenix. You need to rely on the automatic linking or provide your own. You can check that the link is present in the refinement by checking the .geo file.</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Mon, Mar 7, 2016 at 11:06 PM, miyatake <span dir="ltr"><<a href="mailto:miyatake@riken.jp" target="_blank">miyatake@riken.jp</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Pavel,<br>
<br>
Thank you for your e-mail.<br>
<br>
The bonds I want to connect are between CR2 and amino acids like below;<br>
<br>
C PHE A 64 N1 CR2 A 66<br>
C3 CR2 A 66 N LEU A 68<br>
<br>
so I made links by the "make link" of Coot.<br>
<br>
Then I made .cif file by the Ready_Set, but I noticed<br>
it always contained OTX terminator atom of CR2, so the CR2 connections<br>
to the next amino acids were something wrong after refinement if I used the cif<br>
as it was.<br>
<br>
Thus I deleted OTX in the cif file, and then in turn it went well.<br>
<br>
I wonder why the cif file contained OTX, is it something a bug?<br>
<br>
Thank you for your attention.<br>
<span class="HOEnZb"><font color="#888888"><br>
Miyatake<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
<br>
On Mon, 7 Mar 2016 08:40:21 -0800<br>
Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>> wrote:<br>
<br>
> Hi Miyatake,<br>
><br>
> could you please send me (and copy to Nigel) the PDB file (and any<br>
> ligand CIF files you use) and tell what bonds you are expecting to have<br>
> and that brake as result of refinement.<br>
><br>
> Thanks,<br>
> Pavel<br>
><br>
> On 3/7/16 03:40, miyatake wrote:<br>
> > Dear all,<br>
> ><br>
> > I'm trying to a mutant of eYFP, which has fluorescence group,<br>
> > CR2.<br>
> ><br>
> > During the refinement, however, the bonds between the CR2 and other amino acids<br>
> > were cleaved even I added the cif file created by the ReadySet.<br>
> ><br>
> ><br>
> > Would some one give me suggestions to solve the problem?<br>
> ><br>
> > Miyatake<br>
> ><br>
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<br>
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