Hi Pavel,<br>One of the bond angles in the sulphonamide groups SO2NH2 was not correct so had to go into the cif file to correct the bond angle, in another instance -CN bond angles were getting smaller than 180 degree (right after one round of refinement in phenix)  however i was told that these issues have been taken care of in the recent version of phenix. <br>
I will double check my refmac generated cif file and try running phenix refine according to Nigels suggestion.<br>thanks,<br>shya<br><br><br><div class="gmail_quote">On Mon, Jan 23, 2012 at 6:07 PM, Pavel Afonine <span dir="ltr">&lt;<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>&gt;</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">Hi Shya,<br>
<br>
can you explain what exactly the issue is with the elbow generated CIF file in your specific situation?<br>
<br>
Yes, SMILES string is a better input for elbow than PDB.<span class="HOEnZb"><font color="#888888"><br>
<br>
Pavel</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
On 1/22/12 6:35 PM, Shya Biswas wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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>
</blockquote>
<br></div></div><div class="HOEnZb"><div class="h5">
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