I've to add a methyl group to the C-5 of a Uracil base in the 3D structure of an RNA molecule. Please suggest tools to do so.
Pymol can do that better, If you have to add chemical structures to the protein or RNA.
Hi
There are many free available tools for doing direct editing of molecules. I personally like Coot.
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
You have Windoze and Linux versions. You should play a little bit to understand how it works, but it is an waesome.
Another alternative would be to explore if your modification has been already described in some databases like Hic-UP
http://xray.bmc.uu.se/hicup/
Best luck.
Paco
In Coot you can replace you U residue with 5MU (http://ligand-expo.rcsb.org/reports/5/5MU/index.html).
I have been able to add methyl residues using pymol but I guess the conformation of the RNA strand would change after that. Should I run a simulation to check?
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