[phenixbb] "ATP" monomer in phenix_refine

[Nigel Moriarty]

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 <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