[phenixbb] cif files

Shya Biswas shyabiswas at gmail.com
Mon Jan 23 15:28:21 PST 2012

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.

On Mon, Jan 23, 2012 at 6:07 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> 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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