[phenixbb] phenix.elbow and compound refinement

Nigel W Moriarty NWMoriarty at lbl.gov
Tue Feb 16 15:24:34 PST 2010


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.


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
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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

More information about the phenixbb mailing list