[phenixbb] cif files

[Shya Biswas]

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 <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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