Bishwa<div><br></div><div><br></div><div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I am using Phenix 1.0-1069 for refinement and coot 0.7-pre-1 for visualization<br>
and rebuilding. I used SMILES in coot to build the ligand and then merged them<br>
with PDB.I had to do this as a separate step for both chains and the .cif file<br>
so produced was not accepted for refinement.<br></blockquote><div><br></div><div>Why? Can you send me the files directly?</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">


<br>
I used readyset to obtain the restrains for refinement using .pdb file, even<br>
though my refinement works, when i try to run real build refine in coot I get<br>
this error message:<br></blockquote><div><br></div><div>It would be better to generate the restraints using the SMILES in eLBOW and then pass the restraints file to ReadySet!.</div><div><br></div><div>Send me the file and we can fix them</div>

<div><br></div><div>Nigel</div><div><br></div><div>NB. Any files sent to me will be held in strictest confidence.<br><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">


<br>
Failed to match (to the dictionary) the following model atom names:<br>
HB3<br>
“O6” “C10” “C11” “C12” “O7” “C13” “O5” “C8” “C9” ......<br>
That would cause exploding atoms, so the refinement didn&#39;t start.<br>
<br>
Could someone help me with fixing this problem.<br>
<br>
Best regards,<br>
Bishwa<br>
<br>
<br>
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</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>

Fax   : 510-486-5909       Web  : <a href="http://CCI.LBL.gov">CCI.LBL.gov</a>
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