[phenixbb] "ATP" monomer in phenix_refine

Nigel Moriarty nwmoriarty at lbl.gov
Fri Oct 28 14:04:46 PDT 2011


I'm sure Ralf can comment on this but as far as I know changing the
group to RNA makes no difference to the linking.

There is a way to get it to linking automatically if the atom names
are correct and the distance is close enough. You can also try


You have two choices.  The simpler "edits"


or more complex but scalable CIF links




On Fri, Oct 28, 2011 at 12:21 PM, Zhang yu <phenixzyfish at gmail.com> wrote:
> Hi,
> 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?
> Thanks.
> Yu
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

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