15 May
2012
15 May
'12
11:32 a.m.
On Tue, May 15, 2012 at 4:15 AM, Lauren
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. -Nat