[phenixbb] cif files

Nigel Moriarty nwmoriarty at lbl.gov
Mon Jan 23 15:14:04 PST 2012


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



On Mon, Jan 23, 2012 at 3:07 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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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

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