Thanks for your input, noticed that elbow does a better job with smiles rather than pdb files. Shya On Sun, Jan 22, 2012 at 10:34 PM, Kendall Nettles wrote:

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. Regards, Kendall Nettles

On Jan 22, 2012, at 9:36 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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Shya The restraints CIF you sent me which you got from PRODRG has the first line comment (#) removed. Our previous experience with using PRODRG restraints file has been that phenix.refine will read them fine. Did you edit the file? Some of the better inputs to eLBOW include SMILES and PDB ligand eg phenix.elbow --chemical-component=AZM You can also check if there is an entry in the restraints library using elbow.where_is_that_cif_file AZM Cheers Nigel On Mon, Jan 23, 2012 at 3:07 PM, Pavel Afonine 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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