Yu It is most likely that the naming of the hydrogens in eLBOW is using the PDB v3.2 remediated format for hydrogen names. You can get the old naming format from eLBOW using phenix.elbow --wrap_hydrogen_names to create older names. Can you send me both files (from PRODRG and eLBOW) so I can investigate. Nigel On 2/16/10 3:01 PM, YS. Chung wrote:

Dear all,

I am having some difficulties in refining my compound within my structure. I was able to create the compound and the cif file using PRODRG and was able to fit it in coot perfectly fine. However, as pointed out by many users of phenix.refine, the cif file from PRODRG does not work well with phenix.refine. I have created a cif file using phenix.elbow and the refinement itself works fine. However, when I try to use the cif file from phenix elbow in coot, it pulls apart my compound and it's extremely difficult to work with. This still happens when I create the cif file using the --final_geometry option. Is there a way around this or is there something I can do? Any help will be much appreciated.

Thank you, Yu Seon Chung _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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