On 03/23/2017 11:39 PM, Alex Lee wrote:
Dear All,Is there a tool or software which can give Ramachandran information of individual residues in a plot? I used Coot to check for Ramachandran plots, but it shows all the residues in a coordinate I put in Coot, not individual one. I also use "residue info" in coot, it tells Ramachandran "phi psi" angles of individual residue, but it does not show it in a plot, only numbers. Thanks ahead for any input.
Well, you can always AWK out 3 residues and run procheck on them, something like: awk '$1~/ATOM/ && $5~/B/ && $6~/^6[567]/' /a/pdb/pdb2h88.ent >w.pdb procheck w.pdb 1.8 followed by: gs w_01.ps or: ps2pdf w_01.ps acroread !$ (The AWK command will have to be tweaked if fields run together in the pdb due to large numbers or alt. conformations for these three residues) I agree such a feature would be useful in coot. Sometimes you want to know if an outlier is just outside or way outside, or if it is halfway between two allowed regions, and with large, low-quality structures it is hard to find the residue in the crowded rama plot. Clickable points in the R plot fills the bill going one way, now highlighting points corresponding to selected residue would be the other half. eab
w_01.pdf
Description: Adobe PDF document
