Hi Pavel,
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.
I will double check my refmac generated cif file and try running phenix
refine according to Nigels suggestion.
thanks,
shya
On Mon, Jan 23, 2012 at 6:07 PM, Pavel Afonine
Hi Shya,
can you explain what exactly the issue is with the elbow generated CIF file in your specific situation?
Yes, SMILES string is a better input for elbow than PDB.
Pavel
On 1/22/12 6:35 PM, Shya Biswas wrote:
Hi all, 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. thanks, Shya
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