Yu 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 http://www.phenix-online.org/documentation/refinement.htm#anch90 You have two choices. The simpler "edits" http://www.phenix-online.org/documentation/refinement.htm#anch84 or more complex but scalable CIF links http://www.phenix-online.org/documentation/refinement.htm#anch82 Nigel Nigel On Fri, Oct 28, 2011 at 12:21 PM, Zhang yu 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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