[phenixbb] "ATP" monomer in phenix_refine

Zhang yu phenixzyfish at gmail.com
Fri Oct 28 12:21:42 PDT 2011


I had a trouble of refining "ATP" in Phenix. I appreciate any help.

ATP with tri-phosphate is in the 5' end of RNA chain. It is added to the RNA
chain in coot as a monomer "ATP", and it could be connected to the
downstream base after I changed the "_chem_comp.group" option to "RNA" in
the cif file.

But when I refine the model in Phenix, Phenix treated the "ATP' as a monomer
and didn't connect it to the downstream base.

I tried two ways to solve it

1. Add the the modified  (chang the "_chem_comp.group" option to "RNA") cif
file in phenix_refine, but Phenix doesn't recognize it.
2. In REEL, I found phenix has its own cif file for ATP, but the its header
couldn't be edited.

Any suggestions?

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