[phenixbb] Refinement error with Se labeled DNA cif seting

Nathaniel Echols nechols at lbl.gov
Tue May 15 07:32:07 PDT 2012

On Tue, May 15, 2012 at 4:15 AM, Lauren <lauren at gate.sinica.edu.tw> wrote:
> I have a protein complex with 10mer DNA with one adenine labeled with Se-CH3
> at C2’.
> I gave the se labeled pdb structure to the Elbow or ReadySet, the program
> gave me the cif as shown below.
> When I tried to refine the structure, phenix.refine ends with a Error
> message:
> ...
>   Number of atoms with unknown nonbonded energy type symbols: 2
>     "HETATM    2  OP1 AMS A   1 .*.A    O  "
>     "HETATM    3  OP2 AMS A   1 .*.A    O  "

Which version of Phenix are you using?  If it's not the latest nightly
build, could you please update and see if that resolves the problem?
The error message was a bug in the handling of atom names in
non-standard nucleotides, which was fixed a month or two ago.


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