"ATP" monomer in phenix_refine
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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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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
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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participants (2)
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Nigel Moriarty
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Zhang yu