[phenixbb] Refinement error with Se labeled DNA cif seting
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
> 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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