Thanks for your input, noticed that elbow does a better job with smiles rather than pdb files.<br>Shya<br><br><div class="gmail_quote">On Sun, Jan 22, 2012 at 10:34 PM, Kendall Nettles <span dir="ltr"><<a href="mailto:knettles@scripps.edu">knettles@scripps.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">I think prodrg used abc... etcetera to represent different atoms of the same element, while phenix uses numbers. You can hand edit this pretty easily, which is probably easier than editing the elbow produced cif to the correct geometry. However, it is also a good exercise to figure out how to hand correct the restraints at least one time. This is a common problem and we often try both elbow and prodrg, and sometimes neither will get it right for a complex ligand, so it is helpful to understand the restraint file.<br>
Regards,<br>
Kendall Nettles<br>
<div><div class="h5"><br>
On Jan 22, 2012, at 9:36 PM, "Shya Biswas" <<a href="mailto:shyabiswas@gmail.com">shyabiswas@gmail.com</a>> wrote:<br>
<br>
> Hi all,<br>
> It appears that the cif file generated from prodrg (REFMAC format) is not recognised by phenix during refinement. Did anyone have similar issues or i am doing something wrong? somehow the geometries obtained from elbow are not right for my ligand so had to use prodrg to generate cif files.<br>
> thanks,<br>
> Shya<br>
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